Contractor payroll software focuses on paying independent service providers against an authorized amount, such as an invoice, approved hours, or an agreed fee. Enterprise payroll software is built around employee pay processing at organizational scale, including the supported calculations, employee pay inputs, controls, and reporting needed for that environment.
The meaningful difference is the work each process must perform, not simply the number of people being paid. A large company can need contractor payment capability, and an employee payroll suite may include a contractor module. Compare the actual pay relationships and functions instead of assuming the two categories are mutually exclusive.