Some important information from an experiment. Bottom line is after the restart, enabling the exclusions makes this FASTER. And if I disable the exclusions, even after a restart for me, it makes it much SLOWER. I think it is because the slowness is in setting all the error markers, more detail below.
1) With exclusions unchecked, after a restart and do a build it takes a very long time and is status bar says "Setting error markers". I see 695 of them in the "Messages" window (your number may be slightly different, I'm using a newer build long).
2) But when I enable the exclusions, it is very very fast and there are no errors listed in the "Messages" window.
So at least for me in the case of restart, having the 35 exclusions is speeding things up, not slowing them down!
The slowness may be in setting the error markers, which are not there when the exclusions are enabled.