The number notation system is used to objectively factor in player preference of a stage
In a competitive striking system, players will strike the stages they dislike the most while their opponent strikes stages they dislike the most. Once they are done simultaneously striking, you should be left with the middle stage. Since there are 13 stages, the strking order would go like from your perspective:
Player: -6
Opponent : +6
Player: -5
Opponent: +5
Player: -4
Oppnent: +4
Player: -3
Oppenent: +3
Player: -2
Oppenent: +2
Player: -1
Oppenent: +1
Leaving them with only stage 0, aka the stage they didn't disagree to, aka the neutral one.
In terms of MK as a character, his advantageous stages aka his +6 and 5 aren't in the starter list. As a matter of fact, for most matchups, his +1 and 2 and 3 and 4 are also not in the starter list in terms of stages you.
So the striking looks like if you're MK in our current 2-3-1 system:
MK Player: -6
Mk Player: -5
Opponent: 0
Opponent: -1
Opponent: -2
MK Player now chooses between -4 and -3.
The system is designed to objectively factor stage preference prior to the construct of matchups between characters.
Typically the system is used to see if a counterpick system in question is synchronized to be competitively neutral in regard to the current stage list used. As you can see, our current system is not synchronized.
Don't get me wrong, I would love to see RC/Brinnie banned. But if you have claims of competitive neutrality and stage diversity as values, then you can say the following:
We can either make a decision to support neutrality by removing stage diversity
OR
We can make a decision to support neutrality WHILE maintaing stage diversity
The first one would remove rc/brinstar
The second one would remove the arbitrary distinction of starters vs. counter picks stage and would feature full list stage striking.
One removes elements of the game that outside of the scope of metaknight aren't competitively degenerating. The other removes no elements of the game and simply correct arbitrary distinctions on our parts.
I'd defend this in person as well, but I'm done debating it here since this is about KC and not about subjectively deciding on rules.