Can't argue with that combination. I have a 2001 Dodge Ram 1500 with just a cover and a bed mat, no spray in liner. I have done various jobs (gravel, dirt, concrete, furniture etc.) and have used a folded over (3X-4X) old pool cover. The bed is in great shape. The spray in liner will protect from scratches but the bed mat is still needed if there is going to be impacts on the bed of the truck.
I had a weathertech tailgate mat (since replaced) and I believe it has limited value for impacts, looks good however. Review the install guide for weathertech bed mat if you are leaning that way, held down with velcro and I don't believe it is that substantial.
If you are getting a spray in liner there may be issues with bed lights/bed light hole caps. Also if you are thinking of getting the bed rails be aware of the hexagon holes being filled with the liner material. It would probably be best to install the rivnuts first, you could clean out the liner material but thee is a risk of scratching the paint.