A look at the detail of the fares in the Advanced mode of BR Fares, and a bit of "insider knowledge", illuminates what's happened here.
Most fares for journeys of more than a few stops are generally set using 'clusters'. That's to say fares are defined from one group of proximate stations to another, all of them costing the same and having the same conditions. The fares system already has millions of fares - if disparate fares were defined from every station to every other station there would be nearer billions!
In this particular case Bucknell is in a cluster together with some of the other stations to the northern end of the Heart of Wales line such as Craven Arms. For this cluster of stations to the cluster that contains Llanelli, the fares on route 01000 (Any - Permitted, also written as a dot on some systems) are priced in such a way as to suggest they're intended to be valid via Hereford and Cardiff. There are also considerably cheaper fares on route 00839 (via Llandovery) which are obviously for use on the Heart of Wales line.
Unfortunately the clustering system has been used in a slightly inappropriate way in this particular case. The fares along the Heart of Wales line are quite cheap and are priced more like a local journey of a few stops, where the fare depends on exactly how many stations you're going, than a long-distance journey where sometimes large collections of stations have the same fares. Accordingly, the fares from Bucknell to Llanelli via Llandovery would be "too expensive" if they were the same as the fares from the likes of Craven Arms.
To overcome this problem, something called a "fares override" is used. An override means that fares have been set between specific individual stations, which override the fares that would normally apply by reason of the stations being in existing clusters with fares defined between each other. The fares override thereby serves to give slightly cheaper fares from Bucknell to Llanelli than from Craven Arms etc.
It's important to note that fares overrides will only operate where the route of the override fare is exactly the same as the route of the fare that is being overridden. This gives ground to a further issue - the route used for the overriding Bucknell to Llanelli fees, intended for use via Llandovery, are routed 01000. You'll note this is the same route as the route that is used for the much more expensive fares that are intended to be used via Hereford and Cardiff. Accordingly those fares aren't available for Bucknell to Llanelli, so if you want to travel between those stations via Hereford and Cardiff then you have no choice but to get multiple tickets!
If you're still following, this means that there are two routes of fare between Bucknell and Llanelli: 00839 and 01000. This is, in practice, as you say, completely nonsensical. Both are priced for use via the Heart of Wales line after all, just the one that explicitly tells you to go via Llandovery is the more expensive one! So that's how we get to that strange situation of the seemingly less restricted ticket being the cheaper one.
As to whether the cheaper route 01000 ticket is valid via Hereford and Cardiff, that is a further whole question, but to give a very basic simplification - because there are no junction stations between Bucknell and Llanelli, it's considered a "local journey" for which you can only take direct trains, or a route no more than 3 miles longer than the shortest route. The route via Hereford and Cardiff is probably at least twice as long as the route via Llandovery and so it's quite clearly nowhere near within 3 miles of the shortest route.
Hope that helps - I realise my response has got quite long here, but perhaps it gives a bit of insight into why the system presents two seemingly almost identical fares for the journey.
I don't see that there's an anomaly here at all. It's a local journey for the purposes of the Routeing Guide so the route via Hereford and Cardiff isn't permissible.