The reason that it looks shallower is because the nose attitude is higher (there's a higher AOA for a flapless approach relative to that with flaps extended). The higher nose attitude reduces the visual segment (how much you can see over the nose) and it is the visual segment that determines whether it looks steep/shallow to the pilot. To maintain the PAPIs the aircraft is still descending on a 3 degree glideslope and for a flapless approach with a higher approach speed, the rate of descent to maintain that glideslope will be a little higher than that for a flaps extended approach.
This visual picture (in terms of visual segment) applies equally from a 152 to a 737 (where variable flap landings are the norm and the effect can be seen quite clearly).