Firstly, just to clarify, when you travel beyond Waterloo, you may only use BR services, the ticket is not valid on anything operated by LT.
Also, many of the routeing guide maps specifically show Waterloo, rather than London group. In these cases, as far as I can see travel beyond Waterloo is only valid when you are using the shortest route in distance from your origin station to your destination station in London. I can't see that being a problem from the likes of Winchester, but it probably will be a problem from places like Epsom as the shortest route will be via the South Central division.
Thirdly, I don't see any problem, assuming the ticket restriction doesn't prohibit it, of having a break of journey at London Bridge when travelling to Cannon St, Blackfriars or City Thameslink, or at Blackfriars when travelling to City Thameslink.