I know with the Thameslink franchise that the minimum overnight requirements were met but they were badly drafted so there is a gap in the overnight service due to the poor wording of the agreement.
I have mentioned this here before but the wording of the tender is critical to the service that the franchise holder will provide. No doubt as with Luton, Southend Airport would have put its case to why trains should run earlier and later. What influence this had with the tender specification is anyone's guess but with a 9 year agreement now in place if it doesn't meet the airports requirements it will be a long wait before it can be corrected.
We don't know what the last train times requirement are from Southend yet until someone here does a bit more digging are but it would be better for the airport if they are written into the franchise agreement rather than relying on a commercial decision as to what times earlier and later trains actually run.
I would have liked to have seen 4am for a London departure and a 1am for an airport departure.