Yes on my GT I have a rubber washer between the screw head and the cover, on the backside of the cover I have a thick, almost a cork, rubber disk. So the screws never come out off the covers. In fact it takes quite a bit of effort to unthread the disk from the screw. I would do the same for the S. As for my level of OCD that depends on the phase of the moon. My previous work supervisor always called his OCD as CDO to put it in the correct order.Your 26xx S frame would have had m6 0.8 both sides based on the frames I have in same number series so apparently somebody already modified right side to accommodate an available later mounting bolt and probably best to drill and tap original left side to m7 1.0 and get matching bolts else you'll go crazy trying to match them up each time panels are taken off and get one cross threaded and have to do it all then - the snug rubber plugs behind the panels generally do keep the bolts with the panels when panels are taken off but Murphy says they'll get mixed up sometime.
Your option 2 assuming of course that it's OK not to be totally restored to original spec - I do hope you're not that far OCD