If your threat model says that Eve's webmail servers can be spoofed, then Alice can't use webmail at all, or possibly any websites. At that point, the security of PGP in JS is pretty much irrelevant.
I think that is one of the most obvious things that can happen, but no it only affects JS PGP that is integrated on a site you use. PGP in JS is still relevant because it makes it easier to download, verify and execute Javascript "anywhere", not as an integrated solution served by a third party. Sadly.