Some amount of going cross eyed counting tiny teeth later… One Y axis motor with a 16t, one with a 20t. 20t on the X axis as well. Doh! 
More 16ts on order as apparently the one I used was the only one I had kicking about 
Swapped the Y axis motors to be a matching pair whilst I was at it, at least.
Doesn’t explain why the side with the proper 16t was also moving further than expected, though. As far as I can tell the trigorilla board is fixed at 1/16th microstepping - is this correct? Swear I remember reading what the microstep settings should be somewhere in the docs, but now can’t find it for the life of me - can’t seem to find configuration related to this in the firmware, either. Probably will right after posting it - sometimes I gotta reverse psychology my luck… E: ding Searched docs, didn’t search the forum hard enough. This thread has me on the right track, for the reference of any future ratrunners (again. Don’t. just get the kit :p). Already had to customise the firmware slightly because my endstops only have NO pins (yes, sad, switching to NC is high on the priority list)
That Jackpot board looking sweeter by the second…