After recently asking questions of various people in the rail industry it was indicated to me that tickets would be accepted on 'all valid routes', and this would include use of ELL and Jubilee to replace the service between Forest Hill (via London Bridge) and Waterloo East/Charing Cross.
If this is the case then it will mean I will get to work in Waterloo quicker than I do at present going 'over the top', but without paying any extra. Of course this is the only reasonable thing for the train companies to do, but it will mean that the overground services will get a little busier, even if we do get 5 carriage trains on ELL as planned for 2014/2015.