Which parent did the student spend more time with in the 365 days immediately prior to FAFSA being filed? That parent will be the custodial parent for FAFSA purposes, and that parent's information will be reported on FAFSA.
If dad is the custodial parent, his 529 account would be reported on FAFSA as a parent asset.
If dad is the non-custodial parent, his assets would not be reported on FAFSA. HOWEVER -- any money used for the student's benefit from dad's 529 account would be reported on FAFSA as untaxed income to the student in the appropriate year, if dad is the non-custodial parent.
I can't figure out what you're asking in the last question. If by "beneficiary" you mean listed as a dependent on a parent's tax return, it makes no difference at all for FAFSA which parent claims the student as a tax dependent.