And ... so .... what? ... you're not making any relevant point there.
We know just a few scenes prior Protege was going to remake all creation
while simultaneously erasing the Omniversal LT, and Multiversal Eternity,
plus nigh-Multiversal Hawkgod and multi-universal Beyonder.
Until the Scathan the enigma stopped him.
So, whatever the secret reasoning "why" Protege was in-affective once inside the "hourglass"
has absolutely no bearing here since Alice has no access to the 'hourglass"
or Scathan helping her imprison him in it.
ie.
Unless, this is Alice vs Protege after being dumped physically by Scathan into LT's hourglass ...
... utterly meaningless reiterating the same valueless detail.