You're not understanding the deal there. The chips are the same part number, but that is where the similarities end. They have different firmware (code) on them, and that is what determines how most of the pins on them will act and what they can do. It's not as simple as just matching up the part number there. That's like replacing your red Ferrari with a red VW Beetle, and there are even more similarities between those, they're both red, 4 wheels, 2 doors and engine in the back, but would you expect that to drive the same way?
Sony used the same chip in the DS5 controller in the 3 current versions, but you can not just straight swap them between those board revisions as they are connected differently to things on the board, thus also each have their own version of firmware.
The voltages and such are what should have been looked at first before reflowing the MCU. The 3.3v is really about all there is.