Previously, the fare from station A to station B was fairly arbitrary, depending on how many companies were involved, who ran which station, is one a 'London terminal' etc etc.
So, to give two examples, it cost more to go from Crofton Park (zone three) to Elephant and Castle (zone two and one) than from CP to London Blackfriars (zone one, the next station into London from E&C). It also cost more to go from West Brompton (zone two) to Honor Oak Park (zone three) than to go from WB to HOP using two tickets, eg WB to Clapham Junction and CJ to HOP.
But now there are new anomalies... for example, the cost to go from Brockley (zone two) to West Brompton (has to go via zone three, as there's simply no other 'not via London' way to do it) is much less than the cost to go from Brockley to HOP.. the first station you pass en route. (You go through about ten other stations too.) It's also cheaper than HOP - WB, despite being a longer journey with HOP as the first stop.
Clearly, it doesn't matter which zones you go through, only the end points count.