Just so that I am clear on the request, you'd like us to add an option under Company Profile | Batch options under "Validate ledger account", labelled "Force department selection", which would force the user to enter both the account and department as separate operations, even if they selected the "correct" (or at last a valid) account-department from the Finder when entering the account number field.

The option, being in the company profile, would be set on a company by company (not user by user).