Fixes starting window being occluded when enable shell transition

- Fix starting window layer so the layer won't become lower when Shell
is applying finish transaction.
- Fix cannot remove starting window because there were set
mAnimatingExit to true while the window is in transition without apply
exit animation.

Bug: 211045248
Bug: 211844337
Test: enable shell transition, run OpenAppColdTest

Change-Id: Ie05b356048ea2db907704911736f0f93e49eb2e8