I don't know to which Rochford Council memo you are referring and I cannot lay my hands on the Section 106 agreement at the moment. I have found a Rochford District Council document entitled 'London Southend Airport - Operational Controls Summary Table' which makes no reference to a limit on annual passenger numbers.
I believe the 2mppa figure was that used in connection with granting planning consent for the original terminal building construction in around 2010. This has now of course been considerably enlarged under a later planning consent so presumably a higher number was envisaged at that point.