I do not think it's a matter of proprietary header – for what I've understood on these days by digging in the Internet, but I'm not an expert and I could be wrong. I suspect though it is just a matter of verifying checksum of a remote file against a local file: just the checksum, not the Backblaze proprietary header x-Bz-Content.
I think somehow enabling WinSCP to have the SHA1 checksum set in the file info for the file upload. I've tested this in some other SFTP/FTP clients that have it in their Options - and ETag is no more "unverified". But I like WinSCP better and I'd love to solve this. I've seen something like a script, I presume, in your documentation: https://winscp.net/eng/docs/library_example_verify_file_checksum
Could this be the solution? If yes, how could I implement such function into WinSCP GUI? You see, I'm not an expert. Thanks in advance, and anyway I will continue using WinSCP for a myriad of other things WinSCP is really useful for. My best regards.