It's possible to make them autofill, yes, but it's the dialog that asks you if you want to update the password stored for example.com after you autofill, that's the gotcha. That one will set the password for every *.example.com password you have stored, to the one you just used.
edit: Ooops, just realised you were responding about 1Password, sorry.
This is adjustable - sorry for UI in French - https://imgur.com/a/Rn046lL
For a password saved from foo.contoso.com:
First option - "Fill anywhere on site" - this means it will fill on foo.contoso.com and bar.contoso.com
Second option - "Fill only on the specified hostname" - will only fill on foo.contoso.com
Third option "Never fill" - written on the tin.
it's possible to make entries autofill only for the specific subdomain. But otherwise, you're correct.
It's possible to make them autofill, yes, but it's the dialog that asks you if you want to update the password stored for example.com after you autofill, that's the gotcha. That one will set the password for every *.example.com password you have stored, to the one you just used.
edit: Ooops, just realised you were responding about 1Password, sorry.