I'm not sure what your question is. There is no regulationto the contrary. It's more a matter of what's not the basis of this knowledge. There is no regulation prohibiting a pilot from being pilot in command from either seat, nor is there any regulation requiring the pilot in command to occupy a particular seat, while acting as pilot in command.
My reference is no reference, as there's no regulation preventing it...ergo, you can do whatever you like. In other words, unlike Parts 121 and 135, which are beholden to Part 91 and add to it, a Part 91-only pilot isn't bound by the requirement that the company designate a PIC, nor by the restriction that the PIC designated by the certificate holder remain the PIC. Why? Because under Part 91, there is no such regulation.
For operators under 14 CFR Part 91, subpart K, which parallels for the most part 14 CFR Part 135, it's a different matter. Subpart K covers fractional operations, and an operator under Subpart K is issued an operating certificate just like an operator under 121 or 135, and is also issued M Specs, or Management Specifications. These are similiar in nature to Operations Specifications (OpSpecs) issued under 121 or 135.
The answer to your question is that the pilots can decide among themselves who will be PIC and situate themselves as they see fit, because there is no regulation to the contrary. This assumes, of course, that they are not operating under 91K, 121, or 135.