I had a truck with spray in liner. Then last truck I got them to throw in bed liner. I think they all come with the holes these days, unless you buy something really cheap.
I don't overly care either way. If I could dealer to throw in a liner again, I would not pay for spray in.
The hooks might be a little blocked by liner. But I use them all the time no problem. Get some short chains, and leave them attached to hooks. But just today I was using all 4 with ratchet strap. two with chain, two without.
I have had some of spray in come off. Probably from snowmobile carbides. Haven't had sled in one with liner. I saw get whatever.