they do not.. i have both the mft3 and the mft1080 with both fence kits. they are not interchangeable. the two generations are so different they can't even be connected together (rail slots don't line up even after you level the tops to each other).
funny thing is i don't use either of those cross cutting fences anymore. never could keep them square all the time. always had to fiddle with it and never had much confidence in it. i used the mft's perfectly cnc'ed holes for cross cutting with dogs (qwas, parf, rail dogs) for a few years. now i don't even use those very much after tso released their grs-16 track square. i have the pe version which lets me use it on top or bottom edges to get perfect 90 degree cuts. (i have the woodpecker track square too but that requires fiddling too and therefore not 100% confidence in squareness all the time).
save yourself the cost of the mft fences.. grab some dogs or the tso track square and you'll be much happier. keeps the bench top completely cleared too!