In a typical application, the difference between the ingress and egress capture times is important for determining absolute time. The PTP algorithm can use asymmetric information to improve accuracy.
The 1588v2 feature requires that all clock frequencies be known in order to make internal calculations. The clock frequencies should be specified at the time the PTP IP core is ordered in order for the timestamp correction to work properly.
In a typical application, the PTP algorithm (or servo, not part of this IP) will remove jitter over the course of time (many packet samples). It is advantageous for the jitter to be as small as possible in order to minimize the convergence time as well as minimizing slave clock drift.