Perhaps it'd be useful to have a mechanism for plugin authors to include a configuration file (e.g. plugin-check-info.json in the root of the plugin) to give information to Plugin Check?

For example, I'd like to indicate that vendor/phpseclib/phpseclib is a third-party library and hence Plugin Check warnings that recommend using internal WP functions are simply unhelpful noise. i.e. In this example it'd be handy to tell Plugin Check to exclude any checks that purely make suggestions for using WP internals. But there are likely to be many other examples of this sort of thing in relation to 3rd party libraries. A configuration file to declare such items would both reduce noise and still allow developers/reviewers to see what's being declared easily.