Financially I would have thought being in the Welsh Premier would make more money than however many divisions Merthyr are away from the National League. TV rights, more exposure, chance of Europe. I would have thought that, unless Merthyr really harbour ambitions of being contenders for league football, as they were in the 80s, and fund it, their profile and bank balance would be better off being in the Welsh system.
The only issue would be where to put them? Straight into the Welsh Premier would be unfair on those battling to win promotion. Bottom of the ladder would seriously harm the club but fairer on all the other clubs.