Are packages counted as bundles?

Yes it is.

A package will, on its own, not count as being bundled, but if all the games in the package ends up on the bundle list, so will the package (also, if a package gets added to an actual bundle, like the current humble where this is featured, it will also count as bundled).

yes, check it here https://www.steamgifts.com/bundle-games

Yes, they can be if their price dropped too low or they were actually in a bundle.

https://www.steamgifts.com/bundle-games/search?q=saints+row