Yes, it would be fairer to say that principal NSE fares are more expensive.Indeed. The old canard of South Eastern fares being cheaper doesnt bear scrutiny.
Take a day return from Eastbourne to Bognor, a distance of around fifty miles. This is showing at £20.20, and that's without Network railcard or groupsave etc.
Compare that to Leeds to Manchester, a distance of around 44 miles. The Northern stopper fare seems to be slightly more expensive per mile at £19.80 (and much more expensive if the Eastbourne passenger's using a Network Railcard).
The TPE fares something like £27 !
Eastbourne to Bognor is hardly a significant flow, and a good bit slower than the Calder Valley, so not surprisingly the price per mile is low (Pevensey to Havant is the same price, even further for your money) - but Brighton to London Terminals, 51m at £38.80 offpeak is another matter - half as much again as the TPE.