I was also wondering about the cost of mocap when races physique differ largely from that of the actor. I would guess that tweaking these specialised technologies can drive the production cost up very rapidly.
You use short people for mocap scenes involving short people. Something which also provides job opportunities for actors who belong to that minority group. Which is just another reason to include it.
Which helps for one specific size of short race. Which is not necessarily the same as all short fantasy races. Little people in real life don't have a physiology the same as the standard fantasy Dwarf whom are traditionally very stocky and wide.
Even with other races like Imps, Goblins and Halflings there are (Or may be in the case of Halflings which have never made an appearance), overall body proportions are different to what little people have.
To say nothing of races of different biology? Elves that have more elongated proportions? Lizard people (Especially when it comes to facial animations)? Orcs that have wildly different proportions to humans?