Precisely this. How can someone train against a custom variation that they've never seen before, and regardless of the same character, fighting someone else is probably always going to be a different variation, meaning a different unknown matchup.
These problems are not legit reasons to not even try custom. Honestly none if it is broke, the only thing that will come off it is different tier placements and balancing can easily fix that.
As for training against unknown specials that has allready been solved. Ability icons that are displayed on customization screen, character select screen, loading screen and in game below health bars.
Kabal with: NDC, Low Hook and Extended Hook.
Kotal with: Kahn-cut, CG and Totem.
This allows players to know what they are up against and know the matchup. This also helps eliminating counter picking.
All competitive players have to memorize characters moves and this is no different. Right now players are only memorizing the most viable tournament variations and the rest is left for dead.
Many characters mid tier to bottom tier can benefit greatly from custom variations giving them freedom and fixing poor variation loadouts. If anything happens to be broke it needs to be balanced anyways and this is the quickest way to get it noticed. Not in casual online where most players don't even punish -18 moves on block or kotals 41 frame startup sword Pound kissing them in the face.
I for one hope they do this because many characters loadouts are lacking and the Characters suffer from it in many ways.
I think most of the problems are poor loadouts, poor frames, poor Krushing Blow requirements that are causing many characters to lack compared to well rounded characters like:
Sonya, Geras, Erron, SubZero, Scorpion.