Firstly, it's worth remembering that flight testing (or I'd prefer the term T&E) is not just about having the Test Pilots fly it. It is about an enormous team of specialists - with TPs clearly at the core - assess the aircraft.
Presumably most of that team remains at BDN for FJ flight testing - which shows a major potential absurdity of this decision. To take the TPs, who are so fundamental to much of the T&E process, and move them away from the other specialists who rely on daily contact with them to properly assess the airborne system, does not strike me personally as very sensible.
However, also on the subject of military versus civil "certification".
The civil authority (CAA/FAA/EASA/etc.) does not care at-all whether an aircraft is useful to the customer, fit for purpose, sufficiently stealthy, able to maintain secure communications with the ground, or 10001 other things. It is interested in one thing only - which is the basic safety of the system, as demonstrated by compliance with the design code. This can be done by the manufacturer conducting their own programme, providing reports to the authority, and then the authority T&E team cherry picking some key conditions and re-testing. The authority can use their combined information to make decisions about accepability, or about required changes.
The military authority however does care deeply about fitness for purpose, and 10001 other related topics. It also is certifying something about which purchasing decisions are already probably made by the nation's taxpayers, and has a huge responsibility to both them and to the front line operators. This means that simple compliance with a design code is totally inadequate to approve a military aircraft - of just about any flavour, and the relatively simple process used for an A380 would be unsuitable for a Typhoon.
There's much more to it than this, but I believe that this is enough to clearly demonstrate why the UK government needs to maintain a substantial T&E capability.
Whether it's based at BDN of-course is much less important; but, since it's there at the moment and the facilities are excellent for most purposes, the arguments for not keeping it there are unlikely to be seriously considered by anybody.
So what we have here is that a core part of the T&E team for fast jets has been moved offsite. The result will be reduced effectiveness of the whole team, increased T&S costs, and much annoyance amongst people who really should be worrying about "higher things". It seems unlikely to degrade BDN's real role as the centre of UK government aircraft T&E.
G