Yes, they are waterproof.
As for the mounting with aftermarket pipes, I don't see a reason they wouldn't work. Mounting points for the sidecase rack are the bolt that runs through the passenger peg and the fender. The rack runs through the holes that held the OEM blinkers and meets up in a joiner piece that hooks it all together. I relocated my blinkers to the little brackets that originally held reflectors.
Givi designed it to tie into the topcase rack. If you look closely at the pics, you can see the bung where a bolt is intended to go from the sidecase rack to the topcase rack. I didn't want a topcase, so I fashioned the support from the grab rail to the sidecase rack. (Not even sure the support was necessary, but just did it to be safe. Also, it does not touch the bike's bodywork.) This lifted the grab rail up slightly, but I just used some weatherstrip from Home Depot to keep it sealed. If you look closely at the pics, it's not even noticeable. Of course, if you want to use it with a topcase, you just tie it into that rack with the supplied bolt.
I've never used the topcase rack, so perhaps that is the one that requires adaptation to work with aftermarket exhaust. Can't say for sure.