I've been running MOS2 along with some graphite in my auto-tranny without any problems, quite the opposite in fact.
ATF are friction modified to have a low coefficient of friction at low contact speed.
This way, the shifts are smooth. However, these friction modifiers "wear out" quite quickly. This is why the shiffting is more " brutal" in an old fluid and everything is sooo smooth when you just had a fuid change.
By adding somme frictions modifiers, my tranny is smoother for much longer and will wear out less. Sounds like a win-win to me.
I haven't use Molyslip ATS but IMO, this is worth a try.