It's an odd case, definitely. I never realised until relatively recently that Fenchucrch St Station was owned by the LNER, not the LMS at grouping. I assume the Midland ended up with the LTSR for competition reasons - the GER built their own line to Southend, no need for another one. Wikipedia has information on the LTSR being a joint operation between the London & Blackwall Railway, and the Eastern Counties Railway - the latter begin a later consituent of the GER so there was an early link.