Is working for a company that produces software for factory development permissible, taking into consideration the possibility that it might sell this software to alcohol factories?

There is no objection to working for the company as long as it is not confirmed that its intention is to sell its software to wineries and the like. The basic principle concerning a person's work is permissibility, and it does not shift to prohibition except by a confirmed matter, for suspicions do not prohibit what is permissible.