This is good, it suggests that HSI works without problems. However this means that the reason the Arduino framework is not working is only partly becaue of wrong clock and there is something else. Out of curiosity, what if you replace SystemClock_Config() again with the HSE startup routine from the beginning of the thread in the STM32Cube example?
PWM with STM32HAL functions are kind of complicated, requiring the setup of a hardware timer and other stuff. There is an explanation here.
valoros’s answer suggest that it might work now for Arduino after a platform update (either in the vscode update GUI or pio platform update). If not, you need breakpoints at strategic breakpoints during the bootup to see where it goes wrong. Like <user>\.platformio\packages\framework-arduinoststm32\system\STM32F4xx\system_stm32f4xx.c SystemInit(),SystemCoreClockUpdate() or SystemClock_Config() from the variant folder, main() function etc. Also, this define might help?