Toilet flange is too low and needs a flange extender. Should it be installed after the subfloor ( the layer under the cement board for the tiled floor) is in place since it needs to be fastened into the subfloor?
I'd install it after all the flooring is complete so you know exactly how much you need to extend.
You could use one of these extension kits and a wax ring once you know how much of a gap you need to fill. I don't like that the extender reduces the i/s diameter of the toilet drain. I avoid those wax rings with the plastic funnel/flange embedded in them for the same reason. I may just be superstitious, but I don't want to do anything that might restrict flow in that situation...
In stead of a flange extender, these kind of extended seals are also available. I don't have much first-hand experience with them, but I did use one similar to this (if not identical...I don't remember the brand..) a couple of years ago when replacing a toilet on a tile floor in my new house. So far, so good.