This answer confused me, because I saw a different/better behavior. Then I did some tests and saw the behavior you described, but only for player tokens, while NPC tokens were not clickable. Then I noticed that the "Extra selection mode" seems to be broken in that it always resets the (N)PC token back instead of the spell token.
Then I cracked it: If any overlay is applied to any token via an extension (like "Has initiative" or "Wound overlay") then these tokens can directly be grabbed and moved underneath a spell token. The only drawback is that even player tokens get covered after being moved unless the spell token is clicked again. This works for both players and GMs, locked or unlocked.
As a consequence I edited "Wound overlays" to overlay a transparent PNG for the "Healthy" wound status:
https://i.imgur.com/jtr7CxE.gif