Thank you very much for pointing me into the right direction. After disabling SIP, I was able to install as you mentioned.
Thank you also for the hint about the platform plist, so I got my recovery partition working again as well.
By the way: if you have a full backup of your system disk available, you can use this instead of the USB stick. Just boot into it, use
diskutil to check where the recovery partition of your (primary) disk resides, mount it, modify the file and reboot with primary disk. Seems obvious, but sometimes you overlook the simple things.
Edit: also, after disabling SIP, I was also able to run the swupatch.sh script without errors. However, app store never showed any updates (seed or apple production catalog), so I used the modified combo update.
Edit2: booting into recovery partition does indeed work with my non-supported graphics card as well. Once it's loaded, you will see it, just like OSX you simply won't see anything in boot. I just didn't reach that point because I got the "not allowed icon", where my graphic card is not showing anything. Just wanted to clarify this as it's easy to get into this situation with a mac pro and a non-standard graphics card.