I have determined that the translatedPolygon (in red above) being passed to projectQueryGeometry is correct but the returned value of transformedPolygon (in blue above) is incorrect. https://github.com/maplibre/maplibre-gl-js/blob/main/src/style/style_layer/circle_style_layer.ts#L72

Internally, it appears that we're passing some bad values to getElevation (e.g. large negative X coordinates) and getting bad values back (e.g. 0 when the elevation should be ~1000).

I wonder if we're getting tripped up on the mismatch between the maxzoom of the circle tiles vs the terrain tiles?

Before #5599 we effectively returned every circle feature in every loaded tile, so running queryRenderedFeatures on the whole viewport seemed to work. If you had run it on a specific rectangle within the viewport, you would've noticed that it wasn't returning the expected results. That's all to say, the fix goes much deeper than #5599, and touches on some areas where the 3D terrain implementation seems to have never worked properly.