Last night I added ~500 gallons to bring the pool up to a higher level, and added a PVC coupler to gain another inch of height on the outflow pipe (which was indeed spilling out water during fill). I also switched the system back to routing through the spa, since that makes total chemical management easier. And for a bonus, we added an eyeball to the pool return to help with directional flow when that circuit is in use.
This morning, right when the pump started moving water, the auto-fill kicked in to add another 55 gallons. Now I’ll wait a few days to see whether this amount represents the extra water needed to overflow the spa into the pool, or if some other leak remains.