My understanding is, that the configuration is based on the center torso as the only bodypart which you cant change.The Center Torso is what makes the Masakari B the Masakari B (f.E.). You can change all the other bodypars the way they fit, but you still have the same configuration with still just one Mechtree as long as you have the same CT (and it wont be possible to change it) inside.
They also say it: A Configuration is actually the same like a Chassis of the IS-Mechs, just a different name for it!
So you have just one Mechtree for each configuration (like Madcat prime, MadCat A, MadCat

, as for each Cataphract-Variant (Cata 3D, 4X, IM...)
Changing the legs, LT/RT or Arms doesnt result in skilling up a new mechtree! (if it was that way, then omnimechs wont be, what they are supposed to!