There’s nothing that says 3rd parties need to be balanced by company. There’s no evidence to suggest that the dev team thought of that, but rather that it was negligible from the beginning.
Snake and Sonic were added in Brawl, 1 for each company. Snake was added because Kohima asked, Sonic because fan demand. It had nothing to do with making sure Konami and SEGA were even.
Wii U/3DS kept Sonic, added Mega Man and Pac-Man for base roster. This was not in order to balance, but because Mega Man was highly requested, and Namco was helping with the game (Pac-Man is also mf’ing Pac-Man). DLC added Ryu, Cloud, and Bayonetta, which resulted in Capcom having 2, SEGA having 2, and Namco have 1 alongside Square Enix. 3rd party companies aren’t even.
Ultimate adds Snake, Simon, Ken and Richter to base roster. Konami now is tied with Capcom for 3. SEGA has 3 once Joker is added. Square Enix has 2 with Hero. Microsoft has 1 with Banjo. Namco has 1 with Pac-Man.
Not only is it literally impossible for all 3rd parties to be balanced through roster representation, I’d argue it was never a consideration beyond, “We’re not picking 8 Capcom characters because that’s not the point.” But 4 is completely different from 8.
They aren’t going to not add a character from Resident Evil because Square Enix, Microsoft, and Namco aren’t at the same level as SEGA, Konami, or Capcom. It comes down to what the series brings to Smash, not how many slots are on the CSS.
Just pointing this out is all. I don’t think it matters much. If it did, it would already be balanced.