It's been a while since I've had to play with WHM, but I know in the old system years ago you could disable the MultiPHP INI option in the old EA4 configuration. I don't even know if that's still a thing.
There normally wouldn't be a reason to restrict the custom php.ini for a user - why would you want to do that?
You can restrict memory etc and prevent them from running "X" instances, but I'm curious why you would want to prohibit a user using a custom php.ini file