Hi Jack, this is just an observation bearing in mind I'm not an expert in Welsh or in the inner workings of WikiTree.
I think the problem is both Llywelyn (leader) and Llewelyn (lion like) are homophones and would sound the same when spoken and could lose the subtly of the derivation when written.
All of the known Welsh language texts are 13-14th Century or later, so any early documentary evidence will be from Latin, so any difference of name meaning may have been lost through time or misunderstanding. There is also the problem with the obsession in the Middle Ages of 'latinising' everything to give the subject more gravitas. (whoops!)
To maintain the links across the generations, I think the context is the most important factor and I would follow the spelling of the father and note the spelling variants in the comments.
While rummaging around the net I did come across Bloodlines I don't know how accurate it is though.
Steve J