Miah,
You might damage your roof. I had my 88 XJ in an accident and for a while considered taking the total out money vs fixing it. I looked at a 2001 XJ and was suprised to see they changed it over time.
On my 88 XJ I have stainless bars between the side rails. Each bar has a rubber insert to protect the cargo. With the 88 style rack you cargo stays a min of 1/4 or 3/8 inch off the roof. Also the stainless bars redistribute the weight over the entire roof.
On your XJ I believe the bars between the side rails as just plastic held on with 2 sided sticky tape. It might hold the cargo up 1/32 of an inch.
My owner's manual says I can carry 200 lbs on the roof of my XJ, what does your manual say?
I am not sure what to tell you but you may want to pull off your spare and examine the roof. See if you have any metal bending due to the weight of your spare tire. Sounds like you could have paint damage with the tire so close to the paint.
There is a lot of aftermarket stuff out there, sure you could find something that will do the job for you!