Thanks for the reply, Matthew.
While not exactly what I was looking for, it certainly shed some light to the problem. I seem to forget how Archicad can be used differently from what I'm used to.
In the projects I have been working on the modules are usually created straight from the main pln. Typically select-> copy-> save clipboard as module. This will take place at some point, when the plan has some content, but needs modular planning for efficiency. The saved .MOD is then refined and placed in the main plan to it's appropriate locations. So these .mods don't have a real dedicated 'host project' anymore.
What you suggest is that another pln is set up to 'host' the mods (with correct libraries), and if the method I'm familiar with is applied, then copy the module base from main pln into the new one and continue refining it there. This pln can then be used as a kind of module storage, that has no real connection to the main pln, but is merely used to publish .MODs to link to main pln. Sounds worth investigating, as this would solve the missing libraries problem. It also solves another problem; It seems that one Archicad session cannot open more than one extra Archicad for module editing. This can be quite tedious when editing many .mods in a hurry.
And thank you for showing me another feature I never know existed in AC! Until now, I have completely missed the ability to use publisher for module files...