PHRF ratings are "manipulated" by definition, it's how they work; VPP-based ratings are purely data-driven, so are not "manipulated".
How much RC input is too much? PHRF requires distance and time to be measured by the RC. If they get either of those wrong, it will affect the results. VPP-based systems add course type and maybe wind speed (PCS does not require wind speed). I think most RCs can rise to the occasion with a little effort. Again, increased accuracy comes at a cost, which is a bit more work for the RC. If minimizing RC work is the primary goal, then stick with PHRF or OD.
Aside: Wind speed is the hardest parameter to measure accurately and consistently across the racecourse, hence the appeal of PCS. I'm scoring G2P with PCS right now.
Now we get to "the numbers are wrong" statement! What evidence is this based on? What is your "standard"? Crews notoriously sail down to their ratings, and for some, PHRF becomes a crutch. I'm not saying that ORR-Ez ratings are 100% perfect, but PHRF doesn't exactly set a high bar to clear, particularly in differing conditions.
I fully agree that OD is the only unimpeachably "level" playing field in our sport, but this is a Challenge Cup thread.