Just because something is a possibility, doesn't mean it's a probability. For example, Jiggs has 81 possible variants like everyone else. However, no matter which up-b you pick with her, it's still a bad move. Essentially, all the different possibilities with the 3 up-bs are the same since the moves won't be used in any case, so she now has 27 realistic variants. The same uselessness could be said about her neutral-b, leaving her with really 9 builds. Even then, the useful of the different side-b's and down-b's are varying greatly, with there already being a pretty useless option for those moves compared to the others.
She is a special case, since she really hasn't been too reliant on her b moves to begin with, just the occasional rest or slap (though I will admit Melee Jiggs was based around rest.) There are characters like Paletena who have a variety of good moves, giving her more viable builds than most. Then again, she is the only character aside from Mii Fighters that has completely unique customs. A more standard case would be Ganondorf. His customs also give him multiple viable builds.
On average, about half the customs for a given character will be viable. After that, there will be probably around 3 viable builds for each character and one or two builds useful for counterpicks. With 3 real builds for each character, the game will just play like any other game with multiple character options, like Melty Blood's moons or Mortal Kombat X's style options. For the situational cp builds, it's up to the player to learn those builds that will be purposefully used against the player's character(s). If a character has an abundance of viable customs, then good for him or her; it's just a positive trait that the character has. It will be balanced out by the fact that there will be a character stuck to only using 1 or no customs.
Yeah. I know my numbers are arbitrary and the meta could evolve where the average number of competitive builds are higher or lower. It was just to show that it is unreasonable to believe that every variant will actually be used.