Board cert reimbursement money comes from BUMED, so an individual command doesn't really have any yes/no veto power over it. They may not know anything about the process and just say no because they're lazy and indifferent. But you should still be able to get reimbursed. Your specialty leader ought to be able to help. Don't give up on it because the E5 in the MILPERS office says no.
As for the DEA number, are you entering a training program (fellowship?) after leaving the military? You don't need one of your own while in training. You can use an institutional DEA number. The only reason you'd need your own is for moonlighting work away from your program, and that's not part of training or education, so I don't know why you'd expect the GI Bill to pay for it.