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So you if you want the newer bottom you have to upgrade the battery is what you're saying ?

More like the reverse: if you want the new battery you need a new bottom.

The new battery is physically larger, so the old bottom cannot accommodate it.

Oh right but if I want to keep everything but the chassis I can, correct ?

This page has more details, https://frame.work/laptop13pro?tab=upgrade-to-pro. You can keep everything, but they are selling some of the new parts as a kit.