I don't think (but could be wrong) that those tickets are actually valid on the bus - it's an artifact of the Trawscymru buses being entered in the timetable as if they were rail replacements. You got the same thing with stuff like the Oxford-Cambridge X5 when that was in the rail timetable. If it's sold then you could certainly do it on that ticket based on contractual right to the itinerary sold, but you'd probably have to pay the bus fare.
I've played around a bit. The only routes listed on the website as having proper through tickets are the T1, T2 and T6.
The T10 has bus fares entered into the NRE system for one-mode journeys only. Therefore if you search for Bangor to Betws you'll be offered either bus or Any Permitted tickets depending on your itinerary. There is no Holyhead to Capel Curig fare, therefore NRE will find you a combination of tickets (Holyhead-Bangor, Bangor-Capel Curig) to use. If you book Holyhead-Betws however, there is already a through fare (the existing Any Permitted one) so it will offer that - as there's a through fare it won't look to see if it can split it.
The T22 doesn't have bus fares entered into the system. Therefore if travelling between two railway stations with the bus, you'll be offered whatever the rail fare is, including some Advance tickets on Shrewsbury-Porthmadog, but no quota has been allocated for Blaenau-Porthmadog (£61 it is then).
However if you try and go to somewhere that is not a railway station (Penygroes) then the T22 will offer you no fare, only the T2 can do so.
Final bit of madness is that the NRE timings for the T2 don't include Porthmadog or Minffordd so trying to use it to go from Bangor to a destination on the Cambrian will force you to route via Machynlleth because these two opportunities to change between train and bus don't exist as far as railway timetable is concerned.
I applaud what TfW is trying to achieve here - multimodal ticketing and timetabling should be the future - but they've clearly employed Arthur Job to do it. What a mess they've made, both from Retail Pricing and Train Planning.
It was even worse to begin with. You'd look at the platform indicator at Betws-y-Coed as a train approached, and it would say "Bus Station". You'd have no clue which bus station the train was supposed to be going to. The destination was later amended to "Corwen Bus Station", but there is still no way of telling until it's too late that the imminent train isn't going to Corwen (as the sign would have you believe), if you want Corwen you should go outside.