I haven't reviewed this entire thread in detail, so forgive me if I miss something here.
The obvious way to solve your problem (Plan A) is to use an air frame sleeve around the extended motor section, and then design your interstage coupler to accept the larger tube. I have three interstage couplers that go to a larger booster that are designed that way, and I just roll a tube around an air frame mandrel for use in the interstage coupler. In another case, I rolled the booster air frame itself on an air frame mandrell so that it would accept a sleeved motor. I don't know if this ship has sailed for you on this project, but it would work.
I suspect that the motor modification you are asking about would not be approaved. However, I am not sure that this is a slam dunk. I went through this discussion with the powers-that-be back in 2009 regarding the use of a CTI 98mm motor without the integral thrust ring. In that particular case, it was decided that if CTI made a case for me without the ring (the rings were always there on the Gen 1 cases at the time), that it would be considered certified. Some of the discussion points that came up during that time were that CTI would need to make the modification, that they would need to be willing to stand by their commercial warranty, and that CTI and CAR both agreed that the modification didn't affect the performance or safety of the motor. I doubt that removing the plastic that constitutes the thrust ring would affect the motor, so in theory, you might be able to follow a similar path. Plan A would be a lot easier though.
Jim