By using this board you the relevant file is variant_BLACK_F407VX.cpp, where it sets the PLL multipliers for the HSE. You can see that the SystemClock_Config() function that does this is WEAK. So, in your project code, say e.g. src\main.cpp, you can just place a non-weak version of this function where you have the correct PLL settings.
it is apparent that the only thing that changes from thet original code is the PLLN value from 336 to 168, aka half of it (because crystal frequency is doubled). So placing
in your project’s code (in a .cpp file) should suffice.
(Above function is also verifyable or constructable by just letting STM32CubeMX generate the project code once RCC HSE + USB has been configured. It generates exactly the code above in main.c.)
Sadly that’s not nicely macro-controllable to just change some multiplier, the entire function has to be given.
This function does not do LSE / RTC initialization. That is done by separate libraries, namely https://github.com/stm32duino/STM32RTC, which allows you to select the clock source.