Thanks for all the replies. I decided to fill the holes so I tapped them to 1/4 -20 and got some 1/4 -20 plastic screws at Home Depot which I threaded into the holes and sealed in place with JB Weld. I cut the heads off, sanded them flush and covered them with bondo which I feathered in so there is no visible 'bump'. I hope this holds up and any flexing of the roof doesn't crack the paint.
The roof rack suggestions were great but I don't have access to whoever removed it and the hole layout is kinda weird so finding a rack to cover them seems like a long-shot.
If my fix doesn't work I can always the stainless steel screw route.
Thanks again for the help.
If it ain't broke, don't fix it - Don't worry, something will break soon enough for you to fix.