The source doc that defines the standard is:
https://www.med.navy.mil/sites/nmotc/nami/arwg/Documents/WaiverGuide/DODI_6130.03_JUL12.pdf
The section on Feet includes flat feet as a DQ if it is Rigid or Symptomatic
<(5) Rigid or symptomatic pes planus (acquired or congenital) >
I believe JT stands for Jack Test, which is the test to see if flat feet are rigid. If Doc says you have a negative test, and are not symptomatic, then I would assume you won't get a DQ.
If you do get a request from DODMERB for AMI (additional medical info) then you should make yourself VERY familiar with the DODI 6130, and carefully review any info that you send.