It's not about overriding. The JTR only specifies what you get paid. So your commander cannot stop you from getting paid, if it happens. But your commander can order you not to do something that you would get paid for BEFORE you do it, and it would be legal. Then, if you disobeyed, you would still get paid per JTR rules, but you can be punished for not following an order.
Two examples. You have a TDY coming up, leaving from an airport 45 minutes away. Commander tells you to use the base shuttle service to save the squadron money. You're a piece of shit, so you just take a cab because you didn't want to use the base long-term parking lot. JTR says you will be reimbursed for the cab. Commander says you get an LOR for telling her you would use the shuttle. Both happen.
You, a C-17 AC assigned to UPT, want to take a T-6 to San Francisco for the 2017 Brony convention in the Castro district. Commander says the squadron can't afford it. You tell him you and your hetero life partner, a FAIP, will stay at a friend's house in Alameda to save the squadron mad cash. But when you get there, your FAIP mentor immediately finds himself overwhelmed by a deluge of nonbinary polysexual panda-kin sex addicts. Swept away by the raw sexual fury and unkempt body hair of your fellow Brony convention-goers, you decide to each get your own hotel rooms in the heart of San Fran, where the lodging per diem is a conservative $12,500 per night. After returning to Vance in what can best be described as the moistest T-6 in the fleet, you submit your travel voucher. Seconds later, the lights go out, because your voucher was so expensive the squadron had no choice but you use the pot of money dedicated to utilities to fund your pseudo intra-species erotica vacation. Your commander, who for some reason looks just like a certain purple Clydesdale you got way too close to over the weekend, is reasonably upset. Per JTR rules, you must be reimbursed for the lodging. Per UCMJ and AFI, your commander is entitled to rip off your souvenir unicorn horn and stab it straight through your lying heart.
See? Discipline and reimbursement are separate issues.