Given that there's going to be people with season tickets and you don't need to even be on a train which stops where you split tickets if suggest that there'll be a facility for "auto tapping" in that you'll be assumed to have trapped at an intermediate station where there's a split in your ticket based on the time taken from tapping in and tapping out.
Likewise a tap at a station which confirms a change (such as tapping to enter the underground network) would also auto tap for an exit from another station.
Such auto tapping wouldn't be a known part of the system, however could invite additional charges if it's identified that a passenger is relying on them rather than tapping as required.
In doing so you could be charged the correct cost based on if you got a fast train or a slow train or took route A or B based on the services available.
Some may decide to cheat by waiting at a station before tapping out, however given that there'll still be ticket checks, most stations aren't that great to wait at and the very big stations you need to leave the platforms to use the main facilities the level of abuse would likely be fairly small.
Given that you'll have data on those who try it, and those who are likely to benefit the most from such a loophole are likely to be those making the journey often, so you'll be able to direct ticket checks to ensure that these problems ate minimised. You could even direct staff, in real time, to undertake a ticket check within a station to catch those trying to wait for a cheaper ticket who are known to have done it in the past.
With the level of CCTV coverage it would be possible to cross check tap in with tap out and services joined/left in the case of dispute. This would require an assumption that the passenger did the right thing unless there is evidence to show that wasn't the case. This would simplify disputes as there would need to be clear evidence of wrong doing (noisy likely video).
It wouldn't require shifting through hours of video as the tap in tap out times would be known, as would the few services which would have been available and the actual times of those services.
Tap out failure would be fairly limited, and for most people again if there was a unit failure they could be cross checked against their normal route patterns with video checking. This could be done on a £100 penalty with a charge of £100 to undertake such a check (paid in advance), with all charges waived/refunded if the individual was found to have made the journey they claimed to have done (basically, a double or nothing charge), few who are guilty would request such an additional fee be assigned to them.
Again the assumption would need to be that there had to be evidence to show wrong doing.
Whilst this could cause problems for stations with limited CCTV coverage when first adopted such stations are likely to be fairly limited in passenger numbers and you could always send in some RPI's of you think that there's a problem. If there is then add some new CCTV and you'll be able to enforce again, and now easily than at present.