That is some curious! What version of MOI do you use ? 4.0 beat for me

I have not your false result but I can't have the normal result (holes merged) they rest separated! :)

When i redraw a volume (Bolean Diff by a segment ) all works like a charm! :)
I will try with the function chamfer!

https://moiscript.weebly.com/uploads/3/9/3/8/3938813/inset_pilou.3dm