1.4.4. Use Case 4: GPIO Interface Using 3.0V/2.5V I/O Standard - The current version of the Altera PHYLite IP core does not support 3.0V/2.5V I/O standard. - 2025-12-16

AN 756: Altera GPIO to Altera PHYLite Design Implementation Guidelines
The current version of the Altera PHYLite IP core does not support 3.0V/2.5V I/O standard.

You can manually set the pin to use 3.0V/2.5V I/O standard through the Quartus Prime assignment editor.