I've quilted a couple quilts with the combination you are talking about. The only thing I've noticed is that it is a little tighter in my walking foot.
I also did one that was fleece on the top and bottom, with batting in the middle. I probably should have raised my hopping foot on that one, but I was able to work from the front of my machine (custom) and was able to cross the intersections just fine. If I had been doing a panto (from the back) I don't think I would have been as successful.