Wait, so if somebody learns my master password somehow, they automatically get access to every website I've registered in, without even needing to steal my database and such? Not sure that's a good idea.
Scenario A: keyfile is encrypted with master password, site passwords are generated from plaintext keyfile. If the master password needs to be changed, the keyfile is simply encrypted again. The plaintext keyfile remains the same, which means all generated passwords remain the same. No need to change site passwords.
Scenario B: keyfile is not encrypted, both keyfile and master password are used as inputs to generate passwords. In this scenario, any change to the master password causes all generated passwords to change. This would obviously be undesirable.