Chosen Solution

I have good experience with microsoldering so replacing the connector on battery is not problem. Pinout is the same on both batteries. The only difference is size which is not a problem and capacity so the question is will the iPhone 6 battery work with iPhone 6S if I replace the connector on battery? What data is iPhone reading from the battery?

according to Apple’s technical specifications, it shouldn’t make a difference.

I don’t think this will be an issue and if you’re skilled enough to do it, it won’t take you more than a few minutes so the best thing is to try it and see if it works. Then report back so the rest of the community can benefit from your first hand experience.