As a former Air Force squadron commander 40 years ago, that doesn't sound entirely correct to me. There were several guys in my squadron who got their stripes pulled under Article 31 punishments and lost their pay for a time as well. But they didn't desert the squadron.
So if he is convicted of being a deserter and/or a traitor, do the taxpayers get their $300,000 in his back pay returned to the Treasury, for the time he supposedly was "entitled" to that pay while he was playing kissy-huggy with the Taliban enemy for five years?
If convicted, he's got to forfeit that back pay. If not, then that provides a strong incentive to go AWOL and desert and not have to carry out your assigned duties, in exchange for getting a big windfall when you return.
Punishment is authorized under Article 15 (which I think is what you meant - Art 31 is the “Miranda” part of the UCMJ), including forfeiture of a certain amount of pay and loss of stripes. That’s a punishment. Bergdahl hasn’t yet undergone a proceeding at which punishment is authorized. When he does, assuming a conviction, he’ll lose pay and allowances. I suppose there’s some remote possibility of a recoupment action after conviction for desertion, but I haven’t seen it in my 29 years and change active and reserve. 11 more months, maybe it’ll come to pass.