Fix some places that inadvertently removed split root tasks

LaunchParamsController shouldn't change windowing-mode for non
root tasks. Non-root tasks either inherit their windowing mode
from the root or are being controlled in a transient state.

Also, don't remove stacks that are created-by-organizer, it's
up to the organizer to remove those.

Bug: 168770671
Test: atest AssistantStackTests#testTranslucentAssistantActivityStackVisibility
      on device with freeform display
Change-Id: Ibf1e504f04b7aa10dfe2f6976102bcf4836524f1