There is also the issue of the uppermidrange of each humbucker. Like gingataff said, the tonal balance between the Trilogy and the Miracle Man is well suited, as is the Nailbomb/Irish Tour combo.
That being said, I have a Miracle man/Irish Tour combo in my Kamikaze, as I wanted a vintage style neck pup, and a VHII/Trilogy Suite combo in another guitar. Looks like it would work better the other way on paper, but they both sound great and there are no volume drop issues between the pickups.