I see this hasn't been posted to in a while but I'd like to sum up things.
First, I speak from an E39 point of view.
These are not water/weather seals. The caulk/glue/adhesive/whatever-you-call-it is what weatherproofs the glass to the metal. These are covers or if you like, moldings. They provide a clean finished look (when new only, apparently, since most of us have our molding crumbling into nothing).
I've replaced this cover on my front windshield two times. I did both myself. Having plastic wedging/prying type tools is a must. Harbor Freight sells some cheap but very good plastic prying tools.
The rear cover was replaced by a pro and he insisted that the rear glass needed to be removed so he did. I've since seen others here claim that that is not necessary. I can verify this as I went ahead and replaced the rear glass cover myself. Again, plastic prying tools are a must.
I guess I'm getting about 5-6 years out of a cover before it starts cracking, drying up, and falling apart.
Installation tends to go faster than removal as it depends how much things have deteriorated. Pay attention as you remove it...you MUST get all chunks of rubber and embedded metal or you'll never get the new one seated properly.
Sometimes, if the glass has been removed, using too much adhesive can nearly permanently embed the cover onto the glass and make it very difficult to remove. I guess I was lucky with my rear glass--I was able to remove the cover despite the glass having been removed 6 years ago to replace the cover. YMMV.
2001 530i/5 (E39), Topaz Blue/Stone Green/Black (118k miles) *very rare interior/exterior color combo*
2005 545i/SMG (E60), ED Order, Titanium Grey/Grey (lease over)
2014 535d (F10), ED Order Summer 2014: THIS IS THE PLAN SO FAR