If it is UKBF related, as I think it is, then the Government must have been providing this for several months already and as they even agreed to fund this route they must have known and agreed to provide UKBF coverage to DND to enable it to happen. I know the UK Government likes to treat aviation as a nuisance, but pulling away a border guard from a route after promising funding for it seems a bit odd.
The nearest UKBF agents can't just come from EDI though, there must be some kind of customs operation at the port of Dundee, which handles plenty of international ships, who can be freed up for an hour to get out to the airport and back? Right now there are 3 ships heading for Dundee Port from Spain, Singapore and Sweden, as well as Dutch and Aussie registered ships on their way out which must have come in from abroad at some stage. There must be a UKBF presence at the docks.
When they don't release specific details about an issue then people speculate, but it seems neither side want to say what it is that's causing this. The reputation of BE and DND being able to handle international traffic is at stake here.