What is the ruling on selling an electronic system to 'Umrah companies that serve innovative (mubtada'ah) groups and have well-known shirk practices? And does the ruling on selling accounting software to a supermarket that sells halal goods and cigarettes apply to this?

There is no objection to designing programs for Umrah (definition) companies, accounting firms, or other permissible businesses. This is not forbidden merely because it might be used for something unlawful, or because some negative consequences might arise from it. The ruling is based on the predominant aspect of its benefit versus its harm. It is permissible for the questioner to design these programs as long as they do not specifically offer a service for a forbidden matter. The one who purchases them is the one who enters their data.