Answer: IDEA gives rights to the parent, not the student. In a situation like this where the parent’s rights have not been terminated or otherwise legally limited, and the parent is acting as a parent through the special education process, the school must follow the parent’s wishes for anything related to IEPs and special education services, or enter into a mediation/dispute situation. For other education issues, you would follow the McKinney-Vento Act, which recognizes the youth’s rights and actually requires the school to prioritize an unaccompanied youth’s wishes. This is an area where IDEA and the McKinney-Vento Act can clash.
You can be creative to try to support the youth while still following the parent’s wishes related to special education. For example, there’s nothing to prevent the school from providing the youth with additional services the youth wants and needs. On the other hand, I’m not sure what the consequences would be if you offer the youth the services on his IEP, and the youth just doesn’t participate. I’m certainly not advising you to violate IDEA or ignore the IEP. But given that the McKinney-Vento Act requires you to remove barriers to enrollment and retention in school for the unaccompanied youth, you definitely should try to accommodate the youth’s needs and wishes as much as you can without crossing the line under IDEA.
This document goes into more detail and may help, too.