That is the ultimate combo, spray-in liner with a heavy duty rubber mat, which is what I'm currently running for the reasons you mentioned.
I have a model specific Dee Zee heavy duty mat. I use it for a two major reasons. One, it prevents items from moving around in the bed. The other is to prevent the sand paper like spray in liner from scratching up items I put in my bed, like a piece of furniture.
In fact, if I could only have one choice between a spray-in liner or a bed mat, I would choose the bed mat in a heart beat. A mat is all I had on my previous truck, it was there for almost 5 years since new and when I removed it, the bed still looked brand new underneath. Not once did I remove or clean under the mat in those 5 years.