Cleanup check_keys and remove $clusterTime workarounds

In PYTHON-2556 we set check_keys to False in all places. There is some cleanup work we can do now that check_keys is always false. For example we can remove all the
$clusterTime workarounds and remove the check_keys argument for many
internal methods.

We may not be able to backport this cleanup work to 3.12 because the legacy save/insert/update methods have a check_keys argument.