I don't see why this is a big deal -- a native app can also be distributed with malicious patches or dlls, and those are common methods for e.g. game modding an

I don't see why this is a big deal -- a native app can also be distributed with malicious patches or dlls, and those are common methods for e.g. game modding and cracking. If you're worried about the integrity of a program, check the hash.