I can see how that would work great for what you are doing.
However, for general use, the remote files should not change in any way.
A change is most likely a sign that something is not working.
If the flag is automatically set, it would be possible to replace an encrypted file with a malicious unencrypted file. In this case, Duplicati would continue without the user being aware of the change, and potentially restore incorrect data.
I prefer keeping the option to bypass checks as opt-in, so it is possible to work flexibly with the backups, but keep strict checks on by default.