I have been doing martial arts sice 1981, the last 8 years I have been involved in Kosen Ju-Jitsu and I am very familiar with MMA, several of our students have competed at the local level.
I would never wear a kilt on the mat to train MMA/Ju-Jitsu any more than I would wear a Japanese Hakama- it would definitely interfere with my technique while rolling on the mat, and likely get damaged. I can see myself trying to get up while my opponent is kneeling on my kilt, pinning me to the ground; bad for me, bad for the kilt.

If I am wearing a kilt on the street, then of course I have to do what I have to do.

For other martial arts, it might be fine, but definitely not for a style where you are rolling around. Indonesian Silat practitioners train wearing a kilt-length tube sarong and even have techniques that use the sarong to choke or restrain the opponent.

See this link for a cool sarong fighting video:
http://www.coldsteel.com/vdfs.html