If you're unfamiliar with the matchup, can you really call yourself the better player?
MU knowledge extends far beyond just character MU knowledge in a tournament match. Especially when you start attending regionals or higher and you are forced to play many different people than you usually see. MU knowledge extends to stage+character+individual. I've been told time and time again by high level players that you are never just playing the character, you are playing the individual playing the character, and beyond that.
You could know both the character MU and even that MU paired with the selected stage and still get bodied because you have never played the individual before. And although that means you are both at a disadvantage, any unintentional gain (so any gain that wasn't made by skill, just a stroke of luck or whatever you would call it) can completely change the match regardless of skill.
So if anything unfortunate happens and you lose your stock (like say you misread your opponent and get punished hard, losing a full stock super early- total hypothetical situation, but just to give an example), now you are at an extreme disadvantage and you probably have no room to continue trying to gauge your opponent. You literally have to play perfect and hope that you can get some reads on an opponent whose play style you still haven't figured out in the slightest. Which doesn't even make sense because most reads are based off of learning your opponent. And you haven't done that yet.
An argument could be made that you have multiple rounds to learn your opponent and not just your 2 stocks, but that definitely wouldn't hold up because in a tournament you're going to have to re-gauge the MU every time you play a different stage. Which should be every round. So you may never get the opportunity to learn that very unique MU.
So yes, the better player should know the MU. But it may not come down to whoever learns the MU first, it could be the result of someone getting early kills and the better player not even having the chance to come back even if they do finally figure the MU out.
If you have 3 stocks, lose a stock early for any given reason, and then figure out the opponent for that unique MU during your next stock, you still have plenty of cushion to outplay the opponent and comeback.
I'm of course not saying that it's impossible to make a comeback by figuring out the MU in a 2-stock match, it's just going to be much harder if you're playing a higher caliber opponent (higher caliber doesn't have to mean better than you, just a more solid player in general). I came in second at a 2 stock tournament a few weeks ago and in one of my matches I was on my second stock at a high percentage vs my opponent being on his first stock and came back and won both rounds against him after figuring out his game on the stages. But the match wouldn't have been even kind of close if we each had a 3rd stock. It's like Judo said earlier- in a 99 stock match the best player will win every time.