IIRC the original plan would have extended only one MML platform all the way back. Quite a lot of space was lost due to the security requirements for E* and the need without converting the undercroft to provide a wide enough thoroughfare at platform level to the extension.If the original deck had remained intact then there would have been only two or possibly three MML platforms going all the way to the original buffer stops. How annoying would it be if you arrived there and unexpectedly found your train was leaving from a tacked-on extra platform outside the shed, or indeed stacked in one of the very long three platforms ten coaches from the barrier?
Personally it always surprises me that travelators where not installed to link the underground and MML sections better as the current arrangement really does feel like the MML, thameslink & HS1 domestic station may as well be a separate station from E* and underground.