-There is really not enough evidence to support otherwise.
-Season 2 finale: Bob didn't just visit DoppelCooper in the mirror like he has done in earlier episodes, he was perfectly reflected with DoppelCoopers image. Just like Leland's reveal was which indicates that Bob was inside DoppelCooper.
-I've not seen anything from Lynch to indicate that DoppelCooper isn't possessed by Bob in some capacity. His only comments stated that the Cooper seen in the season 2 finale is "not Bob" but instead his doppelganger. What that comment says to me is that he was clarifying to the interviewer that the good Cooper is not possessed by Bob and is instead stuck in the lodge. It doesn't mean that DoppelCooper doesn't carry Bob in some capacity.
-Adding to that, his next comment about DoppelCooper said that Bob was "with him". That can be taken in multiple ways sure, but Bob using DoppelCooper as a vessel is a sure frontrunner for an explantation.
-We haven't Bob possess DoppelCooper directly this season but it would be hard to depict this visually with Frank Silva being dead. The only thing we have to support it is the phone call with Jeffries where he states, "You will go back and I will be with Bob again." That indicated to me that Jeffries (or whoever it was) wanted to put DoppelCooper back in the lodge so that he could be with Bob like DoppelCooper has been for the past 25 years.
-I don't recall Bob being able to possess or be with more than one person at a time which would support my previous claim. Jeffries wants Bob with him, why? Maybe because he's eager for fun.
-Bob doesn't need to DoppelCoop as a vessel, but he doesn't need anything. He wants
Even though it's a pet peeve for you when people refer to DoppelCoop as Bob. There's not enough evidence to support that Bob is not related to him in some capacity. It's perfectly logical to have the theory that you do, but I don't see how we can dismiss other theories without substantial proof.