You should not have any problems passing through Philadelphia Airport with 2 bottles of beer in you luggage. You can fill out your paperwork and unless you have something else to declare use the Green exit doors.
Pennsylvania while having some stranger liquor laws doesn’t have any issues with importing federally allowed amount of liquor for personal consumption. At some point there used to be restrictions on import of Absinthe but most of them have been lifted.
As far as PHL to SFO is concerned the check is not as “thorough” for the lack of the better term.
Credit:stackoverflow.com‘