You can ignore both problems. The 1st one I will make a note to fix. We are not using the HAL timebase, but I can reassign the timebase to some unused timer anyway to make the warning go away (and if we wish to use the HAL timebase in the future).
The other error is because ST make really crap software. I don’t have a solution for this one. However we don’t use the SW4STM32 project file, so actually you can ignore it.
I think you will see that all the relevant files were in fact generated properly, so you should be good.