You are correct it doesn’t work like that for replies, you have to create an alias in the account settings to reply with that address.
The problem with this is that when you create a new alias it generates a public and private key for that address, you can only delete that alias if you delete all the emails associated to that email address. This is where the 15 alias limit starts becoming a problem in Proton Mail.
I would say if you don’t use PGP then use your custom domain with SimpleLogin instead of Proton Mail that way you can get around this issue.
@b-9 Tuta has this functionality maybe give that a look! oopsy didn’t read the whole post x_x