TJarvi,
Welcome! I am always glad to have practitioners in this area join us because it gives other points of view and helps to make us all smarter.
Interesting question! I think the short answer (and not meant to be flip) is they do it that way (PEB decides fit/unfit, EPTS and service aggravation) because the regs state they do. And they probably did that because the threshold question of fitness/unfitness for a particular condition is tied to the other questions (EPTS/SA).
But, to address your other point, I think the VA does have to re-adjudicate the issue of service connection and EPTS even if the PEB found differently and of course that means they have to use the standards more favorable to the veteran. In my opinion, the PEBs findings are only applicable to the Service Secretary's determination, but are not binding on the VA. Getting there may take appeals through regular VA procedures.
What strikes me as bad/unfair/illegal is the fact that under the DoD/VA Pilot program, the Servicemember has no right to a hearing on the issue of the rating before separation or retirement. However, his/her ultimate appeal on the rating issue is handled with a NOD and perhaps BVA or US CAVC appeal. Overall, I tend to think that it is more advantageous for a Servicemember to be in the Pilot Program. But, I also think that the use of this procedure is open to challenge.
The real problem (and opportunity) is that the Pilot Program is less than a year old, so there is no case law out there. However, I think they have inadvertently created jurisdiction in BVA and CAVC for these PEB cases by making the rating determinations run through the VA. In my mind this is a very good thing for those going through the PP.