If the player can customize characters, statistics, equipment, abilities, routes, schedules, or other aspects of the game, the question isn't whether customization exists. The question is what the customization is trying to accomplish. If customization primarily changes the player's interaction with the game, that's something other than a visual novel. If customization primarily changes the story being experienced, that's more of a visual novel.
Stella De's principles for when customization is consistent with a visual novel vs a non-VN game.