The A310MRTT is certified under civil conditions for most stages of flight in the AAR role and for military conditions at others.
For the MCS to 'talk to' the FMS would have required a lot of extra time, effort, downtime and cost to the end users. So the current methodology was derived, where the MCS reads some ARINC data, but does not transmit any. If re-routing or re-tasking is required, the new mission plan can be printed off on the flight deck for the pilots - they may then need to enter new waypoints manually. It all requires disciplined CRM, but works fine.