The answer to this question is the answer to many questions in aviation, it depends. Specifically it depends on the operator's SOP, but the per the FCOM it only specifically mentions leaving the system A un-pressurized if the bypass pin is *not* installed. See FCOM vol 1, pdf pg 106
Based on Boeing's procedures you can have either SYS A un-pressurized or have the pin in, but I'm sure there are airlines out there that call for SYS A to be off regardless of the pin as an added layer of safety or standardization.