Thanks, found it—player_calibrate_height on PlayerBody. Now that I'm no longer hovering above the floor, I see that my table was way too high. I think the player height thing was somehow related to my early failure at scaling the player down to dollhouse scale via world_scale. I don't want to change it back, though; I like that the entire game takes place in a single space.
I think my general problem is that I don't really understand VR in Godot all that deeply. The XR Tools gives some neat shortcuts to most of what I need to do in an VR space, and this works for 99% of the game, but every now and then there's those weird little thing which isn't pre-coded for me—registering a button press, turning the player towards 90.0, rendering to specific left or right eye, triggering a double jump (kinda fixed that), extending XRToolsPickable (screws with XRToolsGrabPointHand) ... probably more. Still, this jam has pushed me to actually look at what goes on inside the XR tools, which I sorta considered to be some kind of overworldly stuff not meant for lesser beings. So things a starting to make a little more sense.