Yes, afaik you can pay out founder wages with Stammkapital.
However, it has to be actual wages, i.e., the founder has to do work in return for a salary, and the salary has to be reasonable. You can't just have the GmbH pay you back the money you put into the company. There are also other limitations (https://dejure.org/gesetze/GmbHG/30.html), but that's the main one.
The difference is shareholder (=Gesellschafter) and ceo (=Geschäftführer). They may be the same person. So paying wages for the work as Geschäftsführer is fine (reasonable amount, taxes, etc), paying out money for being a Gesellschafter is not.
However, it has to be actual wages, i.e., the founder has to do work in return for a salary, and the salary has to be reasonable. You can't just have the GmbH pay you back the money you put into the company. There are also other limitations (https://dejure.org/gesetze/GmbHG/30.html), but that's the main one.