You have a good handle on how the VPP works! In addition to the rough data, like you see on a PHRF certificate, there is most importantly something called an offset file. This is a digital "scan" or model of the hull shape and appendages which the VPP uses in its iterative calculations. The offset file is often acquired directly from the yacht designer. For an "unmeasured" system like ORR-Ez, certain assumptions must be made about displacement, freeboard and righting moment, but this is drawn from a huge database of sistership data. For full-measured ORR ratings, each boat must be stripped-down and weighed and incline tests performed, etc.
The short answer to your question about the Bene 323 DK is that the VPP "thinks" it's a faster boat than PHRF does. Compared to the 375 SD, it's a newer design with higher SA/D, fin/bulb keel, closer winded, etc. Comparing VPP ratings to PHRF is always problematic, because PHRF is based on subjective observations of a certain boat & crew combination. Not to put too fine a point on it, but it's human nature to "sail down" to your rating. Put another way, you only sail as well as you have to, to match your rating. VPPs avoid this subjective element.
That said, I do not claim that all VPP ratings are perfectly accurate, but they're generated consistently and objectively. If there is something the VPP "sees" in the 323 DK that needs to be corrected, it can be done systemically for all similar boats.
Thanks for the questions!