Hi Lang,
SO what Michael was originally talking about, was keeping the seam edge out of the mix, so it doesnt bother the fillets..

Notice in your file how the seam of the cutter goes into the object.



This will create a seam edge in that inner surface and make the fillet more complex.

Here is a file back. I didnt figure out exactly how you placed the original, but this gives the idea. Notice how the seam edge of this cutter isnt in the object at all. If you cut with this object, you can fillet large values.

This seam of the cutter can be controlled in the originating sweep. It's comming from the circles. Rotate them will move that seam until it is on the outside of the cut.