So, I gave up yesterday after I found out that when searching for differences between the original alien loot and this one here i actually compared two versions of this mod - and really, didn't find any differences in the recipes....
So today, a different approach. I have copied the recipes with the balanced settings to the original mod, and this gave some strange results. I have disabled the alien mod4 and 5 plus the lvl 21-80 hyper modules. And then I got error messages from another mod (advanced electronics and potentially boblibrary) that the mod lvl 4 recipe and the lvl 4 mod is missing.
So while I still haven't found the bug with the missing ore, it seems that some other mods look up the alien loot mod and adjust some things, and this might(?) result in the different behavior when it comes to droping ore or mot. Like a mod checks if "alien loot" mod is loaded, and if not it disables the loot.
However this is only an idea. What I will do now (as they other mods want to have some modules enabled which don't exist in your version) is to enable them and adjust the values and reduce their impact.