I found two issues with the latest (and updated) STM32CubeMX when generating a Makefile project for STM32F334 Nucleo64 board.
1. I selected only the LL drivers but the Makefile had the "USE_HAL_DRIVER" definition, so the project wasn't compiling (because there was no HAL driver files in the project as I have selected "Copy only the necessary library files..." in the settings)
2. The SystemClock_Config function had this line which was giving an error because RCC_LSEDRIVE_LOW is a HAL definition:
I had to change it to: