Hi there, I'm having the same issue atm, but I don't really know how to solve it?
Do I need to somehow make MKXP look at the executable directory instead of the CWD? I'm on windows if that helps at all.
EDIT 01/08/21 : Nvm I have figured it out thanks to a different fourm where someone made an unofficial port of Pokemon Uranium to mkxp-z.
Apparently if you are on Windows Unicode pathnames can be a bit buggy, but after renaming the folder to not include any unicode characters (aka I got rid of v13 in the name of the folder I kept the game in) it started up and I can finally play the game now! I don't know enougth about this to fully explain how it works, but if anyone else is using windows and suffers from the "No game scripts specified (missing Game.ini?)" error just take out any Unicode characters that are in the name of the folder the game is stored in and you should be sorted!