I'm not sure why not including the transfer at all is all that much of an issue, to be honest. Not everyone does it by Tube anyway, plenty use buses or taxis, which aren't included, or walk. So the simplest way is just to remove the Tube validity but keep it as a through ticket. As has been said, for a shorter cross London trip contactless could be used which might include it, and for a longer distance trip a couple of quid is noise level, also noting that kids under 11 are free anyway.
You could perhaps set the industry's systems to issue any ticket on ITSO, and if issued that way you'd get the validity. So those it bothered could get an ITSO card, and the rest of us just wouldn't care. Even now I'd rather e-ticket flows were enabled via London even if I lost that validity.
I suspect a lot of people split Advances across London anyway as by doing so you often get more value. This is limiting the issue even further to only rather expensive walk-up tickets. The cheapest Birmingham to Dover single, say, is £62; is £2.40 on top of that really an issue? The next fares increase round might put it up more than that anyway.
To me, the easiest way to find out of people actually do care is just to enable all the missing e-ticket flows* and clearly state on e-tickets that they have no validity on London Underground, and see what people buy. I doubt it would be anywhere near as big an issue as is being suggested. I think plenty will take the £2.40 hit not to have to faff about collecting tickets at the origin station and just use contactless to cross London. It's a bit like the Trainline fee - people on here hate it, but enough people very happily pay it.
* Easiest way to do that might be to run a batch job creating route LONDON NOT UND / ANY P NOT UND tickets for any that are shown as +LONDON / +ANY PERMITTED priced at 10p less than the one including Tube validity, and enable those for e-ticketing.