Hi,
I've run into the same problem you originally had trying to bring up the VC707 reference design on a custom board without the I2C switch, where execution gets stuck in the HAL_PlatformInit() function. I don't see the HAL_PlatformInit() function in the source code so I was going to rewrite it like you did. Since the timer interrupt mask is a parameter for the function, I'm assuming it's used to either enable or disable the timer interrupt; how did you set up the interrupts in your system?