T-VASI has some advantages, see previous thread discussions.
At major commercial airports which operate long body aircraft, the double PAPI installation provides suitable flexibility for a range aircraft types; all in proportion to the runway length etc.
PAPI has an advantage over other systems in that it uses a projected beam of light – a lens / filter system like some old film/slide projectors. This provides a narrower and more powerful beam of light which usually enables an earlier point of contact both in good and poor visibility.
There are many dangers in deliberately flying low (RRR/W). The approach path will be a closer to obstacles or the ground, particularly on short final; the reduced altitude clearance decreases the safety margin in the event of windshear or wake turbulence and will result in a low threshold crossing height with a danger of early touchdown – even in the undershoot. Conversely, flying a shallow slope and then converting to a ‘normal’ threshold crossing height can extend the flare and landing touchdown point with all of the dangers of an overrun particularly on a down-sloping runway where the effects are magnified.
A significant point from the original question is the altitude that any disparity between PAPI and ILS is noticed. In my experience there are few if any mismatches above 100ft; thus a mismatch at 200ft might suggest a PAPI alignment error, an ILS GS transmission error, or that your aircraft has an exceptional eye/ILS aerial height.