I expect TfL are assuming the main interchange stations will be Syd, NJ, WC, CP and NXG where those stations are the first port of call for Southern (National Rail) services on the East London Line.
Although the tube map which showed the ELL extension in the past showed the NR logo on all the stations south of NXG.
In any instance, I expect LOROL will cover the stations not served by the ELL at launch until 2012. (Feb 2011 for the northern extension to Highbury and Islington for NLL, Victoria Line and FCC services to Moorgate) with white cover on platform signs. This way, they don't have to buy new signs in two years time.