In my experience, the most common cause of the Mk7 "running bad" is the dealer service department.
We have GSWs with Phase 1 and Phase 2, and both run fine. Obviously CRUAs and not CVCA.
The emission warranty does not "start" when the last emission repair fix was completed, and is in effect for your car now. As has been discussed at length in other threads, some owners are waiting to complete the warranty work in hopes of getting a new DPF later in the vehicle's life, and to extend the warranty miles/years from the date of their Phase 2 fix. Unless they plan to delete, getting a new DPF with zero ash residue with Ph2b will be a big incentive for those looking for long-term ownership. Phase 2a is only NOx sensor and software, IIRC.
As for dealers, the one's I've dealt with in regards to the Mk7 have all wanted us to come in for anything and everything, including the Phase 2 warranty work. I'm guessing they get reimbursed $ from VWofA and end up selling owners on lots of other "services."
Your question might be best answered by looking through the many posts about "to fix or not to fix" and similar.