If they keep the same battery size while improving the internals, guess what? More battery life.
The batteries the Pro and Pro2 have aren't cheap.
Besides, thermal dissipation. They aren't using 6W chips, they are using 16W ones. Would they gimp the performance and battery life for a mm less or hey, longer battery life!
You're making it sound like an obvious choice, and I'm not sure it's as simple as that. If you're saying more battery life is the priority, then you've compromised the potential performance with that decision. A more efficient chip using the same batteries could be configured to give you slightly better performance with a big jump in battery life, or it can give you a big jump in performance at the same battery life. Many Pro 2 owners are already pretty satisfied with the battery life, so you could justify seeking the higher performance option. The other option is to use this more efficient chip to keep almost identical performance and battery life as it is now, with smaller, lighter batteries. Lots of people would like to see a reduction in weight, so you could also justify this route (although I can imagine some disappointment if the benchmarks didn't improve at all).
So it will be a balancing act. It is possible that they can compromise and improve everything within reason - performance, battery life and a weight reduction. These are the main considerations, I don't think 'is it gonna fit the dock' really influences the design/engineering process until they've decided how they're configuring the internals next time.
They might decide that it would be too expensive to totally redesign the chassis for a small improvement in weight/thermal efficiency at this stage, at which point 'hey, let's keep it the same so it fits the dock' might enter the conversation.