I presume you are using a reasonably recent beta - hence the folder at a time comment.
It is an interesting concern but I think it is unfounded as rclone just does the folder comparison one at a time it should punt the transfers off to be done asynchronously.
I did a couple of checks just to double check and I believe it is working like that.
If you have evidence (logs) of it not working like that, can you post them and I’ll investigate. If it isn’t working properly I’d like to nail it down before the 1.36 release.
First check - 5 directories with 5 files, transfers 15. Snapshot after 2 files have transferred.
* A/1: 0% done, 216 Bytes/s, ETA: 1h20m18s
* A/2: 0% done, 177 Bytes/s, ETA: 1h38m1s
* A/3: 0% done, 0 Bytes/s, ETA: 406h36m42s
* B/1: 80% done, 7.454 kBytes/s, ETA: 26s
* B/3: 65% done, 5.743 kBytes/s, ETA: 1m1s
* B/4: 62% done, 6.639 kBytes/s, ETA: 58s
* B/5: 80% done, 9.751 kBytes/s, ETA: 20s
* C/2: 77% done, 6.326 kBytes/s, ETA: 36s
* C/3: 58% done, 3.378 kBytes/s, ETA: 2m4s
* C/4: 68% done, 6.716 kBytes/s, ETA: 48s
* E/1: 100% done, 12.739 kBytes/s, ETA: 0s
* E/2: 55% done, 2.161 kBytes/s, ETA: 3m29s
* E/3: 77% done, 12.511 kBytes/s, ETA: 18s
* E/4: 62% done, 4.732 kBytes/s, ETA: 1m21s
* E/5: 52% done, 7.730 kBytes/s, ETA: 1m2s
Second check 5 nested directoreis each with 5 files, transfers 15. snapshot after 1 file has transferred.
* A/1: 27% done, 5.546 kBytes/s, ETA: 2m13s
* A/2: 43% done, 5.936 kBytes/s, ETA: 1m37s
* A/4: 43% done, 4.708 kBytes/s, ETA: 2m3s
* A/5: 43% done, 7.314 kBytes/s, ETA: 1m19s
* A/B/1: 43% done, 4.844 kBytes/s, ETA: 1m59s
* A/B/2: 49% done, 13.500 kBytes/s, ETA: 38s
* A/B/3: 24% done, 2.706 kBytes/s, ETA: 4m45s
* A/B/4: 33% done, 4.827 kBytes/s, ETA: 2m20s
* A/B/5: 62% done, 11.425 kBytes/s, ETA: 33s
* A/B/C/1: 58% done, 5.686 kBytes/s, ETA: 1m13s
* A/B/C/2: 40% done, 6.558 kBytes/s, ETA: 1m33s
* A/B/C/3: 43% done, 6.827 kBytes/s, ETA: 1m24s
* A/B/C/4: 37% done, 8.564 kBytes/s, ETA: 1m15s
* A/B/C/5: 21% done, 3.720 kBytes/s, ETA: 3m36s
* A/B/C/D/1: 0% done, 264 Bytes/s, ETA: 1h5m41s