Some people here are in a time warp. The only occasions I have seen squat toilets have been in office buildings where one stall is like this, probably to serve so some old timers who prefer this.
Gas stations have pretty spartan toilets and they can be quite old -- moderately clean, but not sparkling. It's also not fun to wash your hands with ice cold water in Nagano in the winter.
My experience is with male toilets.
The toilet at Shibuya station, although not immaculate, is reasonably clean. Imagine a place like that in Europe.....