I'm running App Layering 2106 with the latest FSL (2105), on W10 20H2 VDAs running 1912 LTSR CU2 and am not seeing that issue. This is my first image with index roaming enabled, and it's still in QA, but I've been testing it for a few weeks now.
What are you doing in each layer for Windows Search? For reference, this is what I'm doing:
OS Layer: Nothing special at all
Platform Layer: Install FSL, set RoamSearch to 1 in the registry
GPO: Enforce the Windows Search service to start as Automatic (though I see it as Manual/Running in my session)