I am hoping that the results of U.C. Davis' clinical trials will help give insight on why some of our TCS cats pee inappropriately. The way I read it, it seems that clean litter boxes really do make a difference (although not always).
I know that cats also pee to "claim territory" - in 2012, when I had shoulder surgery and had to sleep in the livingroom, some kitty(ies) would pee in my room at night - a behavior that I have seen when cats lose their owners.
On a side note - it is similar to coyotes responding to "marked territory" - the old timers here would recommend peeing (yes, human) around property borders to discourage coyotes from entering the yards. I have used it successfully - fortunately, my grandson and his friends loved that chore!