Freedom House is funded in part by the State Department, USNED and USAID and have participated in multiple covert operations and openly biased campaigns. Check the Criticism section of the article you linked and then look into their funding.

Yes, and political scientists are aware of that. Note that much of the criticism is political: China, Russia, Iran.

It definitely favors the west but despite the bogeyman a lot of academics just want good data. It also is not rating the US especially high.

And what would happen if the rated them mich lower? They'd lose their funding and cease to exist is what.