GPGFileTool only permits encryption with public keys which meet some criterion of trust. I'm not in a position to determine just what is required, but certainly locally signing a key is sufficient.
While I understand the risks involved in using untrusted keys, I would expect similar behaviour to that at the command line - i.e. a warning to this effect and the option to cancel or proceed. At the very least, there should be some indication somewhere that GPGFileTool is enforcing this policy, and something explaining how to enable other recipients to appear in the list.
I'm also not sure it should be offering me the option of using revoked uids, but I'm not sure about this. Is this normal behaviour?