Let me just enumerate the levels of protection we have normally
the S3 protocol has sha1 checksums for each chunk transferred
the crypt backend will check the MD5SUM of the encrypted file after the transfer
the crypt stream itself has a very strong message authenticator based on Poly1305 so downloading the data will definitely detect corruptions.
you can use rclone cryptcheck to check MD5SUMs of uploaded files. This has to locally encrypt the file, create the MD5SUM and compare it against the hash stored by S3.
Lets talk about multipart uploads now. These don't have MD5SUMs when in use by crypt because crypt would have to encrypt the file locally first before the upload to create the MD5SUM then encrypt it again. This would be possible (for the local backend) and there is an issue about implementing it.
Given that you still have protection from 1) and 3)
You could use the chunker backend to do this. This can also add MD5SUMs...
However as far as integrity protection the Poly1305 protection is very good, but has the disadvantage you need to download the file to check it.