What if a modpack makes heavy use of keybinds for functions that don’t exist in the base game? If the modpack doesn’t ship default keybinds then all users have to go through and set all the keybinds anyways. If the user has a nonstandard setup like a weird MMO mouse, or custom button mapping to bypass a broken keyboard button, then the onus should be on them to set up keybinds for each game, and I feel like modpacks are distinct games.
For controller schemes maybe there is a way you can encourage modpack makers to support a minimum number of profiles. So if the base game ships with a standard controller profile and a southpaw profile, maybe you can tell modpack authors that they have to support a standard controller profile and a southpaw profile. I don’t think you need to make default controls off-limits for modpacks.