Hey Renato,
I'm new to MoI also and also working on how it does things. As I work on Booleans and fillets I'm finding that it leaves lines that arent part of the object and when you select what you want to fillet, your selecting seperate lines. not the objects boundry line that you want to fillet. What I do is select those lines and delete them, then select again and try your fillet sizes. (The easy way to select lines is to click in the surface which highlights the solid, then point at the lines and they become the "Mode" of selection. Even using window drag!)



By the way, I also did it after the top fillet, though it worked here. (My model may be significantly bigger)
I did think of that before yet forgot it in my process.

Am I correct about the left over lines Michael? I also forgot to mention the original lofting or sweeping lines can get in the way also.