Hi eddi,

We've probably all come across these types of limitations, not only with MoI, it happens in all software, even in cad software that costs 10's of thousands of dollars, I know this from experience and to purchase something for a fraction of the cost of the medium to high end stuff and tell your self why haven't these over priced over bloated modeling software, developed by an army, adapted simple but powerful methods like MoI has.

The thing is when you discover these limitations you plan and work around them until the limitations have been addressed and fixed, the more you use the software the more ways you find to do a particular thing, and when you've established that it becomes easier to find a work around for most limitations.

I've attached your files with all the things that you wanted to achieve with constant fillet by just moving those seems around, so as I was explaining above, now that we know the seams aren't fillet friendly, we simply avoid them, before we commit to a boolean operation we just have to think a few steps ahead and think will the seam get in the way.
What I figured with the 'Merge' command is that if you try an merge multiple sections of segmented edges it screws up the spherical surfaces, but if you do a section at a time it works fine, so you merge the segmented edges of one sphere section at a time.

Until the filleting in the geometry library is further developed to be more robust these are the methods we have to employ.

Cheers