Not necessary only MMU and local institutions, US universities will also accept the Foundation qualification because all they need is your 12th year education (Foundation). Also, certain Australian universities will accept this qualification on case by case basis. I myself got admitted to South Korea's no.1 university (KAIST) with excellent (MMU) Foundation results and exceptional co-curricular activities.

*You will need to send the course syllabus of your program to the universities for them to assess your suitability for admission.

What a conincidence, I was also sponsored by JPA to do my Foundation at MMU but I seriously don't think that JPA would allow you to convert the local scholarship into an overseas one. Your sister will have to look for alternative sources of scholarship if she intends to go for an overseas undergraduate program, probably something like university entrance scholarship. Getting rid of JPA after completion of Foundation studies is completely fine, your sister won't get penaltized for doing that. Good luck.