You don't have to do the VGT delete at the same time you do the EGR delete. When I talk with someone about these engines I tell them to do it as parts fail.
You can do a standard Stage 1 tune on the ECM, I recommend this if the engine has existing warranty left and the customer wants to utilize it till it expires.
You can do the Stage 1 tune with the EGR deleted. If anyone has an EGR valve going bad or is bad.......I recommend that they do a Stage 1 tune with the EGR delete at the moment. The cost of doing this versus fixing the EGR valve isn't that much more and you've eliminated future EGR failures.
The turbo will fail sooner or later in the future, at this time I'd send the ECM back to add the VGT turbo delete and install a different turbo and exhaust manifold.
By doing it this way it will cost more $$$$$ for the complete conversion to a standard turbo over the long haul, but you don't have to pay for it all at one shot. This conversion isn't cheap and to be able to do it in bits and pieces as the emission parts fail is the easiest for people to afford.
I had someone that did an ISX Stage 1 with the EGR delete last week. Jerry called me afterwards to tell me the ECM has a number of recent VGT faults codes stored. With these turbos it not if they self-destruct or fail its a matter of when. A new turbo from Cummins is around $4000 to replace and it will also fail in the future if you run the truck hard. It seems if you do a regional haul or short haul with many starts and stops in a day, you're lucky to get 300,000 miles out of a turbo. The over the road group ranges in the 500,000 mile range between failures.