You’re right, it’s far from ideal.
But the solution does make sense (bear with me). First of all, the outgoing email address can be outgoing-only, just as the receiving address is incoming-only. This allows you to reduce unwanted spam as well as identify the source.
As explained, aliasing is not a solution when you still have to manually set each one up. If Gmail or other platforms could intelligently reply from the appropriate plus-address or dot-address the issue would be resolved but that seems unlikely (not to mention dot addressing is non-standard).
Frankly, I have not had the security issue with replying from alternative addresses explained to me. Surely if we trust the recipient with the (sometimes-private) data they receive, we equally trust them to post. Why not include a token with the email notification allowing any email address to reply (as long as the token is valid).
Just thinking things through here - please feel free to pick these points apart…