The TfW journey planner offers the extended tour via Cardiff as well as the change at Abercynon. I can foresee some interesting discussions at gatelines and on board if they don't fix this by, for example, changing the headcode at Queen Street and splitting the service in two. ScotRail do this on their Fife circle services I believe.
I do not see how there can be any obligation to change at Abercynon so long as the tickets remain routed "any permitted" because a through train between origin and destination station on a ticket is always a permitted route.
However, reading the NRCoT, breaking at Cardiff probably isn't valid, though it's a bit vague and I don't know where (or if) the rules are stated more clearly.
The NRCoT says with regard to the right to break journeys that "this may not be the case with some through services that take an indirect route" (one of the many cases where the NRCoT clearly departs from the pretence that it's an actual contract).
The information box below (so not even pretending to be contratual) says: "For example, where a train service makes a circular journey, you may travel either way to the destination on your ticket. However, you would not normally be allowed to get off at an intermediate station where the fare would have been higher". Which isn't what's happening here but something similar.
Presumably if there isn't anything concrete barring a "change" at Cardiff the tickets could be changed to a suitable routing e.g. "not via Pontypridd" to prevent this.
Pretending to split the service at Queen Street would be unhelpful to someone who wanted to travel, say, between City Line stations and Heath. Presumably a journey planner would refuse to show the through service as the connection time would be too short.