I don't know how you came to that %50 conclusion out of thin air. But no deuce.
It assumes you have 8 (i made this up) viable strategies vs gravity that has a chance to win. Every single strategy also describes what viable decks to field against other opponents. A strategy doesn't mean it should win all matches but it gains you the best benefit under the assumption that every opponent are also fully rational. In that sense a (random) example could be;
Upon inspecting their vault, gravity's possible strategies could be
Strategy 1: field catatians to aether, chargertall to air, dbh to time.
Strategy 2: field dbh to aether, catatitans to air, chargertall to time.
And they know it as well. Then you go ahead and populate for each team. N viable strategies that you think each opponent will use. Next, you build your own strategies (say 8 total).
Then 1 of your 8 viable strategies could be;
Strategy 1: Field psiontall to gravity, Field Rol-Hope to time, Field fractix to air.
Now +1 means deck would win, -1 means deck would lose. This changes when the deck changes (-1 +1 doesn't indicate two results of DECKA vs DECKB. it indicates DECKA vs DECKB and DECK A vs DECK C)
Your strategy 1 could go +1, +1, -1 in case gravity uses its strategy 1, air uses its strategy 2 and time uses its strategy 1, respectively. (why use a deck that would -1 ? because it would win if time used strategy 2 instead.)
This is how you make a game theory table (i made the simplest form with random -+). If you use elimination methods there is no involvement of probabilities whatsoever. If you have no cross eliminated acceptable scenerio, you use mixed method in which case you need to field your decks with slightly controlled randomization.
It has no probability anywhere as long as you assume certain decks counter other certain decks. You cover every possible rational strategy which is viable and aims to win. You could of course complicate things by involving the probabilities of a certain deck winning against another. But i assumed a given deck is generally known to win vs another given deck. (aka RNG is out of this equation because you can't have control over it)