Master Duel uses the standard rules that most people are familiar with, while Duel Links uses the speed duel format, with half the deck size and a three-wide field instead of five
A couple copies can also come in against Esper Control as it exiles Dennick for a single mana
They outplay decks, but they can only have 2 floodgates up at a time, and that means you have to have the correct ones in any given matchup when you need them
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For Commander, I think they are both at the very least solid cards but become much better the higher-power Commander you like to play
WotC believes they wont break the format, relying on Commander Brackets and pre-game talks, and will re-ban if needed