What are you going to be doing with your Jeep? Is it going to be getting wet inside quite a bit? I would tend to worry about the drop in liner trapping moisture and causing rust...especially if the liner moves around a bit and causes scratching of the paint. I have never had one so I don't know for sure, but I do know that this is one of the complaints of the drop in bed liners in pick-ups. If they don't fit well they can cause vibration noises that are irritating too.
I know you have a pretty pristine CJ from what you've described and I can understand not wanting to modify it too much (I am into restoration way more than modification myself) However, if you plan on doing stuff that will be getting the inside wet and/or muddy frequently I think you should re-think getting a spray in liner like Rhino. That is what I am doing after much consideration and research on the subject. I want to preserve my CJ best I can and I am going to so much effort to restore it. I think that that the Rhino is one mod I'm willing to make for the greater good.
Don't know if this helps at all but at least you have a post on here--right?