I gotta go with the cotton to. But only cause it seems to work better in my machine for the FMQ'ing than the polyester does. From all I have learned.. the poly doesn't cut the cotton fabric these days. It used to, but cottons are made better now than then. I'd say to that with the seams of the piecing and the top stitching..there is so many stitches holding everything together anyway that even if one did break...it couldn't do much damage as there'd be 2-3 other stitch "lines" before, during or after the broken one so those would hold things together. I have used poly for FMQ'ing thinking it was a bit more pliable than cotton..can't be sure but kind of makes sense, but then with the thing about strength wins...if you have cotton thread and cotton fabric..there wouldn't be any fighting...
But for some reason the poly breaks in my machine after FMQ'ing for awhile. Don't know why and it has to be the thread as the cotton doesn't break doing the same thing.