Hi Muhundan,
1. The configuration of a STM32CubeIDE project is an ordinary process, which have to made done. Unfortunately there is no other way as including and adding each file after each other. For me it seems more like that you have missed out to add the include paths under 'Right click on project -> C/C++ General -> Includes' ? Could you please check that?
2. Yes you can. The free version especially the resource files are usable in any way you want. You can setup your project with the free resources and later simply replace the libraries by the professional source files.
3. The Platform Package (.msi file) is the addition to expand Embedded Wizard Studio for the underlying MCU family. This windows based file has nothing to do with the libraries, which you use in your IDE Project. When downloading a Build Environment for an evaluation board, you always get all .c/.h files and libs in that Package.
I will discuss that request with my colleagues. In the meantime, please take a look into this thread:
Bring-up on customer specific hardware
Best regards,
Tim