Even frontline commands are handcuffed to HMT - their delegated authority is capped at £100k. Even amounts below this may still have to be referred to HMT if they meet the ever-widening 'novel or contentious' limitations.
The big ticket items are all at the whim of HMT. Even when funded and approved HMT reserves the right to arbitrarily cut funding or delay programmes, even if this attracts additional costs down the line. HMT-induced delays are the biggest additional cost burden on the MoD (I guess they must have a similar death-grip on other government departments, but I have no direct knowledge). HMT-induced costs are always attributed to the MoD and, dutifully, the press follows the usual lines and heaps scorn on the MoD with an artificial belief that there are bunch of senior people in the MoD are moving money around as they see fit within a fixed budget. Even Urgent Operational Requirements have to laid before the Treasury and they don't even have to write a justification piece if they decide not to fund a requirement; a simple rejection will suffice with the operational risk remaining with operational commander.
None of this is new, it just gets overlooked.