Maybe this will help you understand what is happening.
Without checksum:
notebook2:/data/bin$ rclone sync robgs-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/ pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/ --checkers=8 --include=*.nfo -vv --dry-run 2>&1 | egrep -v "Excluded| OK"
2019/01/09 13:01:15 DEBUG : rclone: Version "v1.45-034-gc1dd7678-beta" starting with parameters ["rclone" "sync" "robgs-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/" "pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/" "--checkers=8" "--include=*.nfo" "-vv" "--dry-run"]
2019/01/09 13:01:15 DEBUG : Using config file from "/home//.rclone.conf"
2019/01/09 13:01:30 DEBUG : Escape.at.Dannemora.S01E01.1080p.webdl.h264.nfo: Modification times differ by -202h2m10.534s: 2019-01-09 15:11:05.937 +0000 UTC, 2019-01-01 05:08:55.403 +0000 UTC
2019/01/09 13:01:30 NOTICE: Escape.at.Dannemora.S01E01.1080p.webdl.h264.nfo: Not copying as --dry-run
2019/01/09 13:01:30 DEBUG : Escape.at.Dannemora.S01E02.1080p.webdl.h264.nfo: Modification times differ by -202h2m9.198s: 2019-01-09 15:11:08.021 +0000 UTC, 2019-01-01 05:08:58.823 +0000 UTC
2019/01/09 13:01:30 INFO : Encrypted drive 'pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/': Waiting for checks to finish
2019/01/09 13:01:30 DEBUG : Escape.at.Dannemora.S01E03.1080p.webdl.h264.nfo: Modification times differ by -202h2m7.822s: 2019-01-09 15:11:09.889 +0000 UTC, 2019-01-01 05:09:02.067 +0000 UTC
2019/01/09 13:01:30 NOTICE: Escape.at.Dannemora.S01E02.1080p.webdl.h264.nfo: Not copying as --dry-run
2019/01/09 13:01:30 NOTICE: Escape.at.Dannemora.S01E03.1080p.webdl.h264.nfo: Not copying as --dry-run
2019/01/09 13:01:30 DEBUG : Escape.at.Dannemora.S01E04.1080p.webrip.h264.dd+5.1.nfo: Modification times differ by -202h2m5.643s: 2019-01-09 15:11:11.625 +0000 UTC, 2019-01-01 05:09:05.982 +0000 UTC
2019/01/09 13:01:30 DEBUG : Escape.at.Dannemora.S01E06.1080p.webrip.h264.nfo: Sizes differ (src 3396 vs dst 3390)
2019/01/09 13:01:30 DEBUG : Escape.at.Dannemora.S01E05.720p.webdl.h264.dd+5.1.nfo: Modification times differ by -202h2m3.571s: 2019-01-09 15:11:13.413 +0000 UTC, 2019-01-01 05:09:09.842 +0000 UTC
2019/01/09 13:01:30 NOTICE: Escape.at.Dannemora.S01E05.720p.webdl.h264.dd+5.1.nfo: Not copying as --dry-run
2019/01/09 13:01:30 NOTICE: Escape.at.Dannemora.S01E06.1080p.webrip.h264.nfo: Not copying as --dry-run
2019/01/09 13:01:30 DEBUG : Escape.at.Dannemora.S01E07.1080p.webrip.h264.dd+5.1.nfo: Sizes differ (src 3471 vs dst 3461)
2019/01/09 13:01:30 NOTICE: Escape.at.Dannemora.S01E04.1080p.webrip.h264.dd+5.1.nfo: Not copying as --dry-run
2019/01/09 13:01:30 INFO : Encrypted drive 'pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/': Waiting for transfers to finish
2019/01/09 13:01:30 NOTICE: Escape.at.Dannemora.S01E07.1080p.webrip.h264.dd+5.1.nfo: Not copying as --dry-run
2019/01/09 13:01:30 INFO : Waiting for deletions to finish
2019/01/09 13:01:30 INFO :
Transferred: 0 / 0 Bytes, -, 0 Bytes/s, ETA -
Errors: 0
Checks: 7 / 7, 100%
Transferred: 7 / 7, 100%
Elapsed time: 15.4s
With checksum:
notebook2:/data/bin$ rclone sync robgs-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/ pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/ --checkers=8 --include=*.nfo -vv --checksum --dry-run 2>&1 | egrep -v "Excluded| OK"
2019/01/09 13:06:04 DEBUG : rclone: Version "v1.45-034-gc1dd7678-beta" starting with parameters ["rclone" "sync" "robgs-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/" "pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/" "--checkers=8" "--include=*.nfo" "-vv" "--checksum" "--dry-run"]
2019/01/09 13:06:04 DEBUG : Using config file from "/home//.rclone.conf"
2019/01/09 13:06:11 DEBUG : Escape.at.Dannemora.S01E01.1080p.webdl.h264.nfo: Size of src and dst objects identical
2019/01/09 13:06:11 DEBUG : Escape.at.Dannemora.S01E01.1080p.webdl.h264.nfo: Unchanged skipping
2019/01/09 13:06:11 INFO : Encrypted drive 'pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/': Waiting for checks to finish
2019/01/09 13:06:11 DEBUG : Escape.at.Dannemora.S01E02.1080p.webdl.h264.nfo: Size of src and dst objects identical
2019/01/09 13:06:11 DEBUG : Escape.at.Dannemora.S01E02.1080p.webdl.h264.nfo: Unchanged skipping
2019/01/09 13:06:11 DEBUG : Escape.at.Dannemora.S01E03.1080p.webdl.h264.nfo: Size of src and dst objects identical
2019/01/09 13:06:11 DEBUG : Escape.at.Dannemora.S01E03.1080p.webdl.h264.nfo: Unchanged skipping
2019/01/09 13:06:11 DEBUG : Escape.at.Dannemora.S01E05.720p.webdl.h264.dd+5.1.nfo: Size of src and dst objects identical
2019/01/09 13:06:11 DEBUG : Escape.at.Dannemora.S01E05.720p.webdl.h264.dd+5.1.nfo: Unchanged skipping
2019/01/09 13:06:11 DEBUG : Escape.at.Dannemora.S01E04.1080p.webrip.h264.dd+5.1.nfo: Size of src and dst objects identical
2019/01/09 13:06:11 DEBUG : Escape.at.Dannemora.S01E06.1080p.webrip.h264.nfo: Sizes differ (src 3396 vs dst 3390)
2019/01/09 13:06:11 DEBUG : Escape.at.Dannemora.S01E04.1080p.webrip.h264.dd+5.1.nfo: Unchanged skipping
2019/01/09 13:06:11 DEBUG : Escape.at.Dannemora.S01E07.1080p.webrip.h264.dd+5.1.nfo: Sizes differ (src 3471 vs dst 3461)
2019/01/09 13:06:11 INFO : Encrypted drive 'pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/': Waiting for transfers to finish
2019/01/09 13:06:11 NOTICE: Escape.at.Dannemora.S01E06.1080p.webrip.h264.nfo: Not copying as --dry-run
2019/01/09 13:06:11 NOTICE: Escape.at.Dannemora.S01E07.1080p.webrip.h264.dd+5.1.nfo: Not copying as --dry-run
2019/01/09 13:06:11 INFO : Waiting for deletions to finish
2019/01/09 13:06:11 INFO :
Transferred: 0 / 0 Bytes, -, 0 Bytes/s, ETA -
Errors: 0
Checks: 7 / 7, 100%
Transferred: 2 / 2, 100%
Elapsed time: 7.4s
Cryptcheck
notebook2:/data/bin$ rclone cryptcheck robgs-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/ pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/ --checkers=8 --include=*.nfo -vv 2>&1 | egrep -v "Excluded| OK"
2019/01/09 12:58:35 DEBUG : rclone: Version "v1.45-034-gc1dd7678-beta" starting with parameters ["rclone" "cryptcheck" "robgs-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/" "pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/" "--checkers=8" "--include=*.nfo" "-vv"]
2019/01/09 12:58:35 DEBUG : Using config file from "/home//.rclone.conf"
2019/01/09 12:58:44 INFO : Using MD5 for hash comparisons
2019/01/09 12:58:44 INFO : Encrypted drive 'pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/': Waiting for checks to finish
2019/01/09 12:58:46 ERROR : Escape.at.Dannemora.S01E03.1080p.webdl.h264.nfo: hashes differ (pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/) "ef69e8e0c40be6e7c8d6bd546371517c" vs (robgs-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/) "9436164d4bbfa789f4603d4675b8eb52"
2019/01/09 12:58:48 ERROR : Escape.at.Dannemora.S01E05.720p.webdl.h264.dd+5.1.nfo: hashes differ (pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/) "2d04d9fe505683c2f02d80b66e975083" vs (robgs-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/) "53b9786ebb3cdff90723251f95d2331e"
2019/01/09 12:58:48 ERROR : Escape.at.Dannemora.S01E06.1080p.webrip.h264.nfo: Sizes differ
2019/01/09 12:58:48 ERROR : Escape.at.Dannemora.S01E07.1080p.webrip.h264.dd+5.1.nfo: Sizes differ
2019/01/09 12:58:48 NOTICE: Encrypted drive 'pinagd-cryptp:Media/Videos/Series/Escape.at.Dannemora/Season.1/': 4 differences found
2019/01/09 12:58:48 Failed to cryptcheck: 4 differences found
Without checksum on a crypt it is looking at the modification times and size to determine a dirty file.
With checksum on a crypt it is looking at size and checksum (but the checksums do not exist on crypt so it is just size)
If you look at the cryptcheck results you can see what differences there actually are.
So to answer your questions.
When you specify checksum and they aren’t there, it uses just the size component.
I believe you can try --fast-list. By adding checksum you’ve effectively disabled rclone from grabbing times which according to the docs requires a transaction.
https://rclone.org/s3/#update-and-use-server-modtime