It's all going to hinge on how serious they take this . 72x72 matchup charts are a fucking nightmare in any game, and most games with rosters/options like that only have a few options-
1. Fuck balance and hope(the mvc2 approach). I doubt they'll get that lucky, and in this day and age you aren't going to get the kind of dedication MvC2 got to find out that "yeah theres a real game hidden behind all the trash picks"
2. Limit the differences, which they don't seem to be doing much of. Hellfire scorp seems pretty drastically different from the other scrop. Obviously they'll all share some "core" idea, but if they're going to be that different they'll essentially need to be considered new characters for balance purposes.
3. Accept the differences. Essentially the idea that no character should have a 9-1 matchup across all 3 styles vs ANY other character/style combination, but may have one or two styles that do. So hellfire scorp has a few 9-1 matchups, but all of those are at least viable with sword scorp, who maybe has 9-1 matchups elsewhere. This leads to character picking issues however.
4. False choices. More hardcore version of the above. Basically they just balance assuming a 24 character roster, and assume that each character has a "real" style which they do all their balance around, and then make sure the other styles are inferior enough to not screw that up. Safe, but obviously heavily flawed and probably eat some backlash.
The one thing they've got going for them is they sorta seem to handle balance patching responsibly. I'm not going to say MK9 or Injustice were even close to perfect, but they are receptive to the idea of balance patches. How often games like this should be patched is something you could argue to the end of time(they did seem to overreact to non issue stuff, and then leave serious issues stuff like Kabal) but one very realistic option is to get the game playable through beta testing, and then do a sort of gamma test(stupid name I know) which is basically just taking serious notes for the first 3 months. No matter how good your Q&A and beta testers are, 3-4 months of REAL play with thousands to millions of casuals + tournaments is going to show you more about your game than you ever knew, and if they're smart they'll learn from it and do one big "final polish" patch at the end of 3 or so months(barring "fix now" issues)