For anyone interested, a little more investigation turned up an explanation for what's causing this:
Substance is generating these masks by heavily blurring the Curve map, which introduces seams when nearby edge padding has striped or wildly different values. It's essentially creating similar problems you'd run into if you didn't have enough padding, but in this case, it's caused by the padding method itself. You can test this by loading your curve map into a fill layer alpha, adding a blur filter and playing with the values.
One partial way to mitigate this is by creating your edge padding manually in Photoshop by running the "Solidify C" filter from Flaming Pear (Free here:
http://flamingpear.com/freebies.html ). This still creates lots of seams to fix, but I'll take a partial solution if I can get it!
I wonder if it would be possible in future SP versions for mask generation to be "smarter" by blurring while taking UV seams into account somehow?
