It could be coincidence but it seems to me like they are trying to get people tu burn points for some reason. The stopover flights are similarly priced for points redemption but massively overpriced for cash, for the next 6 months reward flights get SCs. Sounds to me like they are corralling status run folks into using up some of their points, which I assume appear as a liability on the books somewhere...?
I honestly think that's a little conspiracy theorist: a much, much more likely explanation is that fares allowing connections in the routing simply haven't been filed with the VA code yet. Random example ... ADL-KGI. If I go looking for filed fares available in the next few weeks, the only option I see is for QF (all of which show the expected permitted routing, ADL-PER-KGI).
So, when I go to request ADL-KGI on the VA website .. what's happening is that Sabre can't find a published fare ADL-KGI, so it looks for logical ways to get there and finds: ADL-PER on VA, followed by PER-KGI on VA*XR .. same routing as QF, but two separate fares (and thus ridiculously expensive).
Guessing this will be fixed soon - VA revenue management just need to file a whole stack of fares with connecting options to do so.