Well, RTW battle models are basically M2TW strat models when you look at complexity (I sometimes joke about "Rome Total Clone War") if memory serves you might be able to copy them straight from RTW battle into M2TW strat.

The reason for multiple groups is the more advanced use of optional\randomized model parts and varied, shared textures which was first was used in M2TW version of the Total War series. With it comes a totally new set of coding to make that work properly.
Strat models have only one group because they have no coding need for multiple groups (it simply won't function), not even weapons. So why spend an hour coding the same stuff all over if you can just merge all groups (after deleting duplicated groups on more advanced models) and do one coding?

From the look in the pic the leg isn't the only part that glitches, looks like it's rigged to the cloak bone I spoke of or another unsuitable bone. There is a standard position for weapons in Milkshape (M2TW use) which looks off when you use asymmetrical weapons, like the blade being horizontal and the edge pointing away from the model. For it to look proper the joint of the hand also has to be correctly positioned on the model.