At the time being in order to manage (Add, Set, Remove) mailbox folder permissions programmatically you have two options:
1. Use Exchange Online Powershell, which is slow in bulk operations
2. Use EWS, which is faster but depreciating and based on Microsoft will retire in 2026
Please confider adding commands for mailbox folder permission management via Graph.
It would be significant improvement for large enterprises which use custom built self service tools.