Scrivener v3 open to project
Control-F to bring up Find/Replace box
Alt-Tab to go to another app
Another app brought to the front but Scrivener Find/Replace box stays on top instead of going into the background with its own app
That is true. It is an oddity. Though I imagine not technically-technically a bug-bug, but something in the way Qt works, were I to guess.
With two Scrivener projects open, they share the same Find dialog or panel, including the last search terms. Other panels, like keywords and bookmarks, stay with their specific project, as you’d want, and they also stay with the Scrivener application window when you switch to a different program. But opening “Find” spawns a new taskbar item. But then, the Find panel has to actually read and work with the contents of the editors, which is surely more complicated than what the kw and bm panels need to accomplish. But would that make it necessary for Find to remain on top when Scriv itself was not? Maybe we’ll find out! 
I haven’t found this to be much of a problem/annoyance compared to some of the other dialog/panel behaviors in Scrivener (and held over from S1, at that.)
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