A few topics come to fore here. Collaboration. IP. Evolutionary complexity.
None of them mix well. More over, I expect you are about to find the hard way, as I've suggested at several times, once you start with multiple developers or worse, multiple teams of developers and you introduce "business stakeholders" it get exponentially more complicated extremely quickly.
I would echo those who have said, "DO NOT FIGHT ECLIPSE". Your choices are to abandon it or learn to make it help you. You can hybrid the projects, we tend to run hybrids in work with independant git, java, maven and eclipse (or inteliJ) build contexts. When you set up and maintain so many projects in Java/Eclipse/Maven this doesnt even strike one as complex. In context of your case, this would amount of adding your own custom "parts". I note you already have a post build factory script.
On learning eclipse, cube mx, ST Cube IDE. It breaks down to this:
Core Eclipse + CDT C/C++ Developer toolkit plugins <-- these are best downloaded as a pre-configured bundle which deletes most of the Java stuff for you too.
Then you add on top a handful of STM plugins. These are embedded panels and tabs in various locations throughout Eclipse customized or entirely bespoke to STM.
Cube itself is just a stand alone application which they have embeded into Eclipse now.
The VAST majority of those multi-gb files are source code, examples and documentation. If you were to strip those folders back to what is the actual IDE it would be about 400Mb tops, probably half that is IDE cruft too.
Eclipse itself is not that hard to learn and a lot of what you need to solve is already configurable with it or by adding plugins. If Eclipse won't help you, add a custom Make file or Sconscript or CMake and get eclipse to call it when you hit "Build". Hybrid approaches can have side effects and work arounds, YMMV.
Try this for example. Go and download a Vanila C/C++ CDT Eclipse IDE. Follow a guide to add the toolchain to it yourself! Get it to compile HelloWorld.a and link it into HelloWorld.exe Without all the clutter from STM32 it should help you learn a little about what is Eclipse and what it will do and what are the STM complications.