Hi,
it's an not expected usage case!
The default hotspots have set distorted=true by default - this means the hotspots will scale with the pano zooming, but the default hotspot scale is 1.0 and made for normal 360x* panos.
A flat panos is internally defined as pano with a 1.0 degree horizontal view, so the default zoom for such panos is very high by default and this leads to the large hotspots.
Best regards,
Klaus