The implementation is wrong. You should test what happens which prefix has priority if more of them are present. @phpstan- should always win.

I just copied what seemed to be being done for @psalm-, for which the only place I saw priority logic is in PhpDocNodeResolver::resolveTemplateTags(), for which I put @phan- at a lower priority than both @psalm- and @phpstan-. The test case here seems to confirm that.

As I mentioned, feel free to update the PR. Or, if you want to point out specific test cases where @phan- is overriding @phpstan- (and where existing @psalm- doesn't have the same problem), I'll try to take a look when I have time.

Thanks a lot!