Hello Jay,
There are two things you should pay attention to. The first one, is to click on update button at project generation window. The second one is to keep the same name as us. When you save your project, you can change only the path.
We are working to get rid of these limitations, but for your understanding, for the ESC example we already provide the IOC in the installation path, and we copy & update it with your new motor parameters, it is why it is important to click on update button. Otherwise, the workbench re-generate an iOC from scratch without the PWM input control.
I advise you to re-do the exercice in an empty folder, without changing the project name, and clicking on update button (instead of "generate").
Regarding the compilation flow, even if cubeIDE is not working out of the box yet, a workaround is proposed in the Release note, section :" Working with STM32CubeIDE for Motor Control projects"
Hope it helps
Cedric