It's my understanding that that only 3 shifts are definable.  We are using Evo for both Labor and Payroll and have defined a first shift and a second shift.  Even though our first shift people start at varied times, we deduct lunch from 12:00 to 12:30.  For our afternoon people, we deduct lunch at a time that all of the people are there.  While we know there may be a disconnect between the job that someone was working on and the job that had the lunch deducted, it wasn't a material difference for us.  Like you said, it's not worth the extra clocking.  We are using a touch screen pc mounted to the wall near the employee entrance and our team scans their barcoded card to clock in and clock out.
 
It's working very well for both purposes.

If the Start and Buffer are the same, then Evo just uses the Rounding value in WO defaults for creating shift entries.  We have 1st shift defined as starting and ending at 1:00 AM with a buffer of 1:00 AM.  We have people who start at 4:00 AM (by choice) and people who start as late as 7:00 AM who are all on first shift.   We don't deduct for breaks, so it's just lunch we'll deduct for.  Whatever job they are clocked into at noon will have 30 minutes deducted.  It has not been and issue for us.  It is Important to update people's shift assignment if they move between shifts.  If they are not clocked in during the time that their shift breaks for lunch, their hour total will be off.
 
We use 15 minutes as the rounding default.  Shift transaction will always begin and end on a quarter hour for payroll purposes.  We don't round labor transactions so actual time on a job is in the work order bucket.  For payroll, we reconcile job hours and shift hours to monitor how much time is unaccounted for.  After some education, we really don't have many issues.