You don't need permission or a license. You just can't distribute the rom. What you can do however is make a patch of your new custom rom that can be applied to the 'stock' rom. This patch would contain no copyright assets. It just makes it slightly harder for the layman to do. But if they've got a rom burner then they can probably figure out how to apply the patch. It's not hard.

There's a guy who has done this for a bunch of games. hook and TFTC come to mind. He's done a bunch of others too though.

No he didn't. PPS doesn't own any Data East rights.
https://www.pinballcode.com/

Providing software patches is well established to be legal. PPS can threaten people if they like but they don't have a leg to stand on. If they did try to do any legal action there's a good chance the EFF would step in to defend the author.

Additionally you can still get the LED ghosting patch for WPC games. That hasn't been removed.