Now I understand the background of your question. In principle, the specifications of the STM32CubeIDE are only suggestions, how you handle your projects is ultimately up to you.
CubeIDE therefore suggests having a workspace into which you import your projects, but which remain there after you close it (without deleting it).
If you are now working on a project, it may well consist of several sub-projects, which can all be loaded into CubeIDE at the same time. You can then compile each one separately, for example, or all of them at the same time.
When starting CubeIDE, you can select the workspace to be used, which is based on the version number of CubeIDE by default. Of course, you also have the option of using a separate (CubeIDE) workspace for each project (be it one with one or more subprojects).
The only catch is that the CubeIDE preferences and development artifacts are also stored in the workspace as defined by STM32CubeIDE, so it can happen that CubeIDE behaves differently depending on the workspace selected.
However, you could also set up the file structure within the (CubeIDE) workspace in such a way that you first create your personal (sub-) workspaces as folders there, in which the respective sub-projects (one or more) are then located. This would have the advantage of keeping the above settings in the same (CubeIDE) workspace.
There are even more ways to organise your work. The best thing to do is to familiarise yourself with the philosophy of Eclipse so that you can find your personal structure.
BTW: The project structure you listed is typical for the case:
IOC > Project Manager > Project --> Toolchain/IDE = STM32CubeIDE (Generate Under Root)
...which means .project, *.ioc etc are stored at the root of the project folder, not in the folder CubeIDE. If you create projects for other target compilers (IAR, Keil, etc) with the external tool STM32CubeMX, a named subfolder is created in the project (EWARM, MDK-ARM, etc).
You also have the folder Debug, possibly later also Release, both of which contain the respective files: generated object code, map/list files, ELF, possibly also BIN or HEX files. Everything in Debug and/or Release can be deleted or omitted without any problems during the backup, because it can be restored from the source codes at any time. If necessary, you can still save the source code for quicker access.
Regards
/Peter