Hi @JackNXP ,
Thank you for your interest in NXP Semiconductor products and for the opportunity to serve you.
Could you please tell me of the versions of the MCUXPresso IDE and SDK lib.
Which SDK example or operation are you referring to?
InitBootPins() is the default pin_mux initialization entry point generated by the config tool, while InitPins() represents the specific operations generated by the config tool based on the configuration.
I did a test for your question.
IDE: MCUXPresso IDE 25.06
SDK: SDK_2.x_EVK-MIMXRT1064 25.06
When I add an LPI2C1 peripheral by using the Peripherals Tool, the I2C pin initialization is performed by BOARD_InitPins() instead of BOARD_InitBootPeripherals().


Wish it helps you.
If you still have question about it, please kindly let me know.
Best Regards
MayLiu