Is it permissible to work on comparing an automated system for a company with the system of an industrial bank that deals with conventional loans and Islamic transactions, knowing that this comparison does not address loans, and does not guarantee the bank's purchase of the system?

There is no Sharia impediment to comparing the two systems, because the bank's work is not limited to what is unlawful. Your work in comparing the two systems will be in the area of current accounts and will not touch upon loans. Furthermore, your task will be limited to recording the differences, and your work will not necessarily result in the bank purchasing the system.