I recently had the rust cut out where the sunroof joins the roof, but the rubber seal has a gap about 1cm where it doesn't quiet meet up......

am I missing something or has the rubber seal shrunk?

PS. it was also like this before the rust got removed.

 

The rubber seal is just to keep debris out.

Water can get by, but it is channeled to the 4 corner drain tubes.

If the gap bothers you, just fill it with black RTV.

 

he is right, there is a gap in mine too, nothing to
worry about unless its starts comming off the sunroof. new seals are very expensive, so take that into consideration. Lates Matt22

 

should the gap be at the front or back?

As before I got the rust out it was at the front now its at the back.....

 

you'd probably prefer it at the back, just in case it's not flush (perfectly), you won't have any noise,

 

my gap is in the front and dont really notice any extra noise, then again my exhaust doesnt let me hear much of anything. lates Mat22