I did setup domain1 in Configuration-> Other-> WebAuthn TFA
and added a WebAuthn authentication to the user.
The user was able to login.
Then I changed over to domain2 and logged in with TOTP.
I did change to domain2 in Configuration-> Other-> WebAuthn TFA
and added another WebAuthn authentication to the same user.
The user was able to login with domain2, but as expected not with domain1.
Then I changed Configuration-> Other-> WebAuthn TFA
back to domain1 and the user was able to login again via domain1.
This means to me, that I can change between domain1 and domain2 in Configuration-> Other-> WebAuthn TFA
back an forth and each domain which is currently set in Configuration-> Other-> WebAuthn TFA
works with WebAuthn, without re-registering a key after a change.
This also means to me, that it technically should be possible to change that on the fly by Proxmox, depending on that which domain I am using to connect to it.