I think you are registering it on the wrong form. As you correctly said in your first post, this is a used vehicle so needs a V55/5 not V55/4. V55/5 requires much less type approval information, though it does ask for a type approval number. I'm not sure about this, because when I was registering ex-MoD vehicles most were types built before type approval was introduced and it was before the IVA regime came in, but as a vehicle built for use by the military, it should be exempt. Certainly whenever I registered an ex-MoD vehicle I just put 'not applicable - ex-MoD' in the type approval box and it was never a problem. Alternatively you could try the GM type approval for the base vehicle or it might have to go for an IVA.
Is there a (common) confusion here between unladen and gross weights? Though type approval includes kerb weights etc, the weights which are relevant for licencing (driver and vehicle) are gross not unladen, so is the fact it weighs under 3500kg as it stands relevant?
My guess is that if the suspension is unchanged from GMC original there will be no change in gross and axle weights and the original figures could be obtained from GM. If Penman changed the suspension to cope with the armour, they should have gone through a documented design process and you should be able to get the relevant figures from them.
As I understand it, it's perfectly legal to drive it to a pre-booked MoT and get it tested on the chassis plates provided it's insured. Make sure when you book the appointment they record the chassis number. Certainly that's what we always did, after having checked the situation with DVLA, VOSA and the police.
Having said that, it would be worth checking as there have been so many re-interpretations of the law lately. I know at least one person on here had a problem with an over-zealous policeman in these circumstances. If you do check, I'd do it with VOSA or a senior traffic officer rather than believe an MoT tester or a local DVLA clerk. You may of course feel that trailering it is less hassle!