It would seem thru my "testing" and subsequent completion, it only counts momentum stacks on tuskens on the end of battle.
I've used Chieftain L, Shaman, raider, SLKR, KRU and won with only SLKR standing, getting no credit despite having more than 200 stacks on a single tusken at numerous points of battle.
However, when completed with tuskens alive at the end, used full Tusken team chieftain L, momentum feat was granted and max box obtained. I replicated this one every third tier, so my results are accurate to tier 3, tier 6, and tier 9. My tuskens cannot survive tier 10, so no testing was done there.
Perhaps this helps support pinpoint where the issue exists as it doesn't seem to be how many stacks its counting, but rather when they are counted.