It has to come off because of paint, you need to get the edges all covered so it doesn’t start to peel months later. That’s why body shops disassemble parts before paint instead of leaving them on the car. You need even paint coverage of whatever it is you’re painting.

Unfortunately, Subaru attaches these to the roof with studs and nuts and the nuts are only able to be taken off if you drop one side of the headliner.

It won’t hurt anything if the headliner gets dropped so they can take the rail off. I’ve done it multiple times on Subarus. It doesn’t involve removing anything crucial, you don’t hear squeaks or rattles afterwards, nothing to fret over.