Don't use non-generic tuple etc. in stubs

[JukkaL]

Many test fixtures use class tuple: pass or similar for list/dict (there may be others) even though these classes should be generic. If the corresponding Instance isn't generic, mypy may crash in some cases. We'd like to be able to assert that these are always generic without breaking tests. We should update the fixtures to make these always generic.

More discussion at #3305.