Yes. Employees can use multiple punch methods for different punches throughout a shift.
As long as all the devices involved are online and connected to the cloud portal account an employee can punch in using one method (timeclock A), punch out for lunch using another method (smartphone app), return from lunch using another method (timeclock B), and punch out using another method (web portal).
The employee's status should update in the cloud portal with every punch. The events should be recorded on the employee's timecard and displayed on related reports.