When R' Chaim (or any other Rosh Yeshiva) explains the Rambam with a Brisker lomdus is that really what the Rambam meant?
The שרידי אש in both a teshuva and a published letter says no. He writes that it is clear that the Rambam's derech was not R' Chaim's. All you have to do is look at the Teshuvos Harambam where he deals with some of the issues/contradictions. The Rambam never gives any lomdus to explain his psak, rather he gives what we would call Baal Habatish answers. He had a different girsa in the Gemara, their copy of the Mishne Torah was wrong, he made a mistake, etc. Not once does he employ anything close to Brisker lomdus.
What does this mean for us? Does it matter?
The answer would seem to be it doesn't. This is the way that Torah works. The Mishen Torah as a sefer has been accepted and meaning can be found in it even if that was not the Rambam's intent. Call it whatever you want (רוח הקדש, סייעתא דשמיא), the great sefarim take on a life and meaning of their own.