If you want to play motion you need good offensive flow (passing), and good jump shooters on every position. A good example is my cup finals, against the 2nd best team in CBBA (someone can argue that is the 3rd, but again very strong league team for Cyprus), using motion my PF killed his PF, with very good %. We got also almost the same rebounding rating. The same happened on our league game:
(27349736) and this:
(27349616), If you also go on last season the results are similar. So a zone, especially 1-3-1 zone could have huge effect on those games, plus the lack of the OD that most big men have could put them easily on early foul troubles. You can see that with my C who doesnt have OD all, and see how much is fouling against good JS big man.
Also one very good reason that i am using motion offense instead R&G, is exactly that is giving lots of JS on the big men.
So the reason that 1-3-1 works against motion is more about the bad execution from your opponents than the D.