current version 0.31.2 and interacting with a remote app (WVD Published App) window does not invoke fancy zone operation either by dragging or keyboard shortcuts
this window is currently being dragged

to confirm the actual remote desktop application window which displays the available subscribed services does invoke fancy zones:

windows version 20H2, Build 19042.804

Please let me know if you need any more information. I've just got a UWQHD monitor and Fancy Zones is an absolute must-have.