Always update layers when building a finish transaction

- Deduping layers across different transactions can result in
  inconsistent application of layers, especially when building the
  finish transaction for a transition which is expected to restore
  the container's state properly

Fixes: 409392394
Flag: EXEMPT bugfix
Test: atest WindowContainerTests
Change-Id: Id4c1c49ecb58b9f19718cb926f1ff2d76d791ad7