That occurred to me too subsequently. I don't have any specialist knowledge and I haven't even read TFA, I just like studying engineering problems.
To alter the buoyancy there are four main possibilities as I see it. Alter pressure. Alter volume. Alter gas mix, Alter temperature.
The delta pressure that could be achieved is limited by the structural and hermetic integrity of the gas envelope. It's probably quite feasible to build an envelope capable of pressurisation above atmosphere to perhaps 1 bar which would certainly give you a good range of buoyancy control and I think an operating ceiling of 5000m, possibly more, based purely on range of alitudes where neutral buoyancy is obtainable.
Volume changes could be effected with some kind of mechanical bellow. But as this results in a delta pressure it's similar to the above.
Temperature change is the most promising mechanism. Additional lift could be created using hot air balloon principles. You would get fairly fast reaction control
Gas mix changes would allow for trim changes as the craft ascended or loaded / unloaded. It's easy to conceive a system of pressurised gas containers that can be selectively opened to adjust the gas mix. Nitrogen would be the obvious candidate for this. But the problem lies with recovering the helium. Unless you can fit a scrubber system that can selectively leach the gas and return helium, under pressure to the onboard storage. If this device leaks helium - and it almost certainly will - then it is a) evil and b) useless.
But I appreciate this machine is a hybrid and most of the buoyancy issues are taken care of by generating aerodynamic lift. However, they would want powerful trim controls so at least some of the above must be designed in to the craft.