If I have plugs I don't know it. I just reinserted the bolts when I removed the bars. I figure I'm not going to misplace the bars and have a much better shot at not misplacing the bolts if they're still attached to the vehicle.
I did the same as you, except that I cross-threaded one and couldn't get it in all the way, and it was too hot out for me to try to fix it so it's staying that way for now.
So if memory serves there are a total of 3 positions for cross bars, diagramatically from above, something like this
front
x x
x x
x x
back
Where each x is a position with 2 threaded inserts where a pair of bolts can go.
My car came with the fore and aft crossbars installed with black torx shoulder bolts, and in the middle unused positions there were these nice silvery torx shoulder bolts.
I'd rather get a few more of those silvery ones for all the now unused locations.
[I'll try to remember to take and post some pics this weekend]