If that was a concern when you got the Line-X standard, then you should have upgraded to the Premium version (missed opportunity for the salesperson), that one is supposed to be thicker & softer on the knees. Saying that, I had the standard Line-X spray in my last truck and I have never had an issue with it scratching items stored in back. Your furniture should not be rolling around the bed anyway, so no reason for anything to scratch? I never felt a need to have a bed mat on top of a liner; granted there are a whole bunch of you that feel it's needed, but a quality spray-in liner will protect the bed as-is.
One word of caution with the horse mats...they off-gas horribly, so if you park in a garage, it is going to stink for a while. Those are big in the home gym community and that is the #1 complaint. If you don't have a tonneau cover and the bed sits in the full sun, that may help get rid of the smell sooner...but something to keep in mind. Of course, that would be another reason to get the Premium version of Line-X, as it has UV protection. I had a tonneau, so the standard was fine before and will be on my new Ram.