Cool!
I'll try using the decrease fillet size trick later tonight!
My quick checks right now tell me I still get problems, but maybe I shouldn't rely on booleans too much... but it's so fast and sweeeet! :)

Just for reference, I attached a small test I was working on, I can fillet one of the parts, but not the other (the lower part in this case)
I tried the decrease fillet size as well on a couple of different boolean surfaces of this type :o)

Cheers!
Jens