The main issue is the platform capacity at Waterloo. Especially on the "suburban slow" lines
That comes in to it, for sure. Many years ago there was a draft plan worked up for the main sub side as a result of TfL wanting to cherry pick certain routes, and once those routes had been isolated (on paper) at Waterloo, the usual four platforms that were required for most of the off peak day, the number of platforms required for all main sub trains increased to six, due to the longer turn rounds resulting from keeping stock (trains) on specific routes.
From a crew perspective (AFAIR) the depots that were most involved with the main sub, Waterloo, Wimbledon, Woking, Guildford, Strawberry Hill (and others eg: Staines etc) to a lesser degree, all signed the various routes, so even with a change of timetable that kept stock on specific routes, platforms permitting, you'd still have crews changing trains, primarily at Waterloo, as under the rules for repetitive working there are only so many times any given crew can work over the same route in succession before they have to work to somewhere else. And then there is the issue of all those depots maintaining route knowledge over all routes!
It was always the case at Waterloo that services operating the three groups, Main Sub, Main Line and Windsor, were kept separate from one another stock wise as a general rule, although some interworking was necessary in and around the peak times, due as you rightly say, to platform availability, and the crew diagramming detail is largely governed by the stock working plan.
