Maybe a bit of nail polish on the holes or if you have some, take the bolts out put some form-a-gasket on the holes and put the bolts back in while it is wet. Seals it up and acts a bit like locktite on the nuts and bolts.
That would be a long shot to cancel the MODs altogether. How many shiny painted tops do you see on the Jeeps? Quite a few. Far more Painted than MIC in my neck of the woods anyway. Maybe even more painted Jeep tops than soft.
No, not negative. Yes to using it a lot for cars, obviously, because that type of trailer isn't "very flexible" (loose cargo like dirt, rocks, etc). So the investment is large.