Covering at least four US Administrations, it's within the range of normal for the State Department passport application status to not be representative of the actual status of the passport application. I wouldn't worry about it.

That the USPS tracking system is off with passport applications after arriving in PHL is also unfortunately not a surprise and also is most often indicative of no real delay in the passport application resulting in the passport getting back to the applicant.

If the check has cleared with the funds out of the current account, then I wouldn't even give this a second thought and just assume the passport would be back in the same range as other applicants whose online status updates were more timely/accurate.