I've used them for awhile now, never had any problems. I can even just spritz the marks, and dab at them with some scrap batting and voila! they're gone.

I haven't. Crayola Ultra Clean is designed to be water soluble. They were formulated to be able to easily remove from children's clothing (i.e., fabrics). I would be super cautious & test them on silk or silk blends, but I've had no issues getting them out with cotton, wool, linen & poly fabrics and blends of those fabrics. They've been out for a couple years now & I've been using them almost since they first showed up in my local Target.

The regular washable (non-Ultra Clean) markers do not always wash out; when I have heard people complain about "Ultra Clean" markers here on QB, every time it turned out they accidentally bought the regular Washable markers, not the UC markers. With UC, sometimes it's taken me as many as 3x to wash out certain colors (yellow, usually) entirely if it's been sitting on the fabric for a long time, but they always come out completely. If you fall asleep & leave them soaking overnight, the color might be temporarily picked up by light colored fabrics (can you tell I'm speaking from experience? -- oops!) but you just toss in a Color Catcher & soak/wash it again & it all comes right out. I've never had any color return or heard of anyone in my guild who had that happen. We've had people complain about the blue pen, purple pen, Frixion pens, a variety of pencils & colored chalks either not coming out or bleeding, but I've yet to hear any issues with the Ultra Clean markers.

There are only 4 things I would ever use to mark a competition quilt:
1) White chalk/ceramic pencils
2) Actual white chalk
3) Crayola Ultra Clean markers or crayons
4) Golden Threads

A hera marker would also work, but my eyesight isn't good enough to be able to see that.

PS -- I routinely iron my quilt top after marking it & have never had any issues removing the marks from Ultra Clean markers.

Something that concerns me about marking the top before layering is that sometimes I want to iron the top, especially when layering batting and backing with washable school glue. I like to use my iron to set the glue and get a smooth surface. For that, I'd want to mark after layering. Also, if I mark a border and then want to do any ironing while applying the binding (depending of the method I'm using) I could set the markings with the heat since the quilt hasn't been washed yet. So I think you might find youself using a variety of methods depending on the project.