You recognize, of course, that if the "legal substances" do many of the same things the "illegal substances" do, then all we're talking about is which particular compounds have been added to MLB's list - the metabolic effects would be the same in either case; the ethics of use would be the same in either case. The question that's being begged here is, why is a given substance banned, if a very similar compound that behaves the same way, yields the same benefits, is not banned? Why is it perfectly OK to use dietary supplements that have identical, or "very similar" effects to banned supplements? That's essentially saying it's OK to use substance X until MLB finds out about it and adds it to the list.
Put more simply, that's saying it's OK to use anything, if MLB doesn't yet know about it/hasn't banned it. So...what's the point of banning any of these things? It becomes an unending "arms race" between the users (no, not the chemists - the users) and MLB, and it is, frankly, a joke. MLB's not protecting its reputation, and its not protecting the players' health, either - they'll just move on to the next compound, which may be more dangerous than the banned ones.
So, IMHO, it kind of looks like they should just stop pretending...stop testing the players, let 'em take whatever they want. That seems to me to make more sense than what they seem to be doing now - which is punishing the stupid/careless ones.