OK, I’ve figured this out at least partly. ctrl-shift-comma and/or the ProfileGPU command actually do run a GPU profiler even when you’re outside the editor, they just don’t pop up the GUI. If your game is connected to the UnrealFrontend, you can see the text version of the profile in the console:
I’m guessing there’s still a way to get a GPU Profiler GUI to display this data, but I haven’t found it yet. If anyone knows how, please let me know!