Overall that looks easy to solve:
I would think that in any rationalisation for pay-as-you-go, it would make sense for the via Redhill and via Sevenoaks fares to become equal, with either route being permitted.
Looking on brfares.com, I see you're correct that there are also via-HS1 tickets. Frankly, I'm a bit baffled by that. Outside times of disruption, I can't envisage any way that it would seriously make sense to travel from Tonbridge to London via HS1: To do so you'd either need to head right out to Ashford, or change at Paddock Wood and then again at Strood, neither of which looks like to me like a sensible route - so I'm going to hazard a guess that sales of Tonbridge-London via-HS1 tickets are close to zero. But at any rate, I can't see either of those causing an issue for Project Oval: Ashford is unlikely to be included in the Oval area, so anyone going via Ashford would have to buy a paper ticket anyway. And for anyone using HS1 between Gravesend and London, presumably you'd just apply a premium to pay-as-you-go fares, which will be very easy to detect and apply because of the separate HS1 gatelines at St Pancras International and Stratford International.