Assuming that ref_clk is in normal as the cause of the internal PLL not locking, is there anything other than the power supply that could be causing this?

The reasons why the PLL does not lock can be summarized as "input clock," "reset," and "power supply.
If this is happening only on a specific board, if no abnormality is found in these three points, the PLL itself may be damaged, etc.

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Category: Specifications
Tool: Quartus® Prime
Device: -