in my experience, and I have a similar situation in my home gym as the OP - ceilings too low for the press, on your knees would be a back killer. You aren't going to get as stable a base as being on your feet. I never actually tried it though, but considered it and thought it wasn't worth trying.
I substituted the OHP with the Z-press, which is sitting on the floor with your legs spread. I have also found that if I sit facing into my rack, I can brace my feet against the lower cross member and that allows me to push against the rack and stabilize my midsection more.