Gonna answer my own question instead of removing it, should someone search for the same thing.
Even though it is commented in the SConstruct config file, that to generate the compilation database scons version 3.1.1+ is needed. That comment should not be taken for granted and even in the follow up configuration it is checked for scons version 4.0.0 before using the compiledb tool.
So long story short: Make sure you're environment does have at least scons version 4.0.0