INV-LCY does seem an odd choice, I heard the rumor was the aircraft would op LCY-INV Slot1/AM then op INV-XXX-INV and back to LCY Slot2/PM.
That would kind of make sense as the only morning flight from the London area TO Inverness is now the EasyJet Luton flight, the Easyjet LGW-INV doesn't leave LGW until midday so not much use for passengers traveling from London to do a day trip to INV.
It would be a shame if the INV-AMS service were to be dropped once the funding runs out in September but who knows BE may have a change of heart.
The rumour about BA re-invigorating the LHR service has been around for a while (wasn't it dependent on LHR getting a 3rd runway I seem to remember Willie Walsh saying).
BE setting up shop at LCY rather than LHR, where there is the potential for pax as well as point to point, is part of the tragedy of not expanding LHR.
Airport charges are not the issue (LCY's are high, like LHR's), it's the price of slots on the secondary slot market because of the shortage.