Air pig
The £5000 is correct, and you can bet the MoD costs will be a bare minimum profit margin, remember the crews and aircraft are already a paid for asset and civil operations are paid as 'aid to the civil power'. So a percentage is from the MoD budget supporting civil AA operations as flight crew pay engineering and command and control are paid from the defence budget.
what exactly do you think will be different under UKSAR? The aircraft and crews will already have been paid for and the DfT will, if required, be recompensed by the NHS for providing something (hospital transfer) that is not covered by the core contract ( and it is only your supposition that it isn't).
Any financial transfer will be between govt depts and not directly with the contractor - remember DfT are are responsible for providing UKSAR and they pay the bills. Frankly no different to transfer of funds between MoD and NHS at present.