Neither of these sound natural.
The difference between "he made them understood" and "he made them to be understood" is that the former means 'he' was directly responsible for ensuring others understood, whereas the latter means it was just his intention that others understand and made efforts to make the message understandable.
The problem with your examples is when you bring in the superlative "the most" - it doesn't seem appropriate in the context. You use a superlative in a comparative sense - something might be "the most understood" when compared to other things that are not so easily understandable.
I think what you mean to say is that 'he' deliberately made whatever it was understandable so that most people could understand it. You could express that by saying:
He made them to be easily understandable.
He made them to be widely understood.