I think the issue is not so much whether someone will put their quilt in the freezer, but the fact that the ink stays in the quilt.
If it's not acid-free, the ink could cause damage that we won't know about until a couple of years down the road.
I tried 8 colors of pens and (I think) six colors of highlighter and all of them do come back when exposed to cold. (and of course, quilts shipped in the winter time DO get exposed to temperatures cold enough to make the markings visible again)
It would be a little embarrassing to mark your whole quilt top for FMQ and press out the markings only to have it show up at your sister's house in Idaho covered with the markings for quilting. ;)
But, the markings all washed out of white fabric with a quick hand-wash and didn't return after they were pressed dry and put back in the freezer. I scribbled pretty heavily with the pens, so I'm not concerned that the much fainter lines that I use for markings will come back.
I wash my quilts when they're finished so I'm sure they'll be fine.