CM has been updated a lot lately. My SO 3 goes directly to the back from the last cut when a job is finished. Mine does not go to the home position. Now if I pause and then stop it goes to the home position. That is normal behavior. Maybe on newer machines it goes to home so hopefully others will chime in to the behavior on newer machines. Not sure if at the end of the job that a pause would work to keep the Z from returning to home position. You might try that. Then when you get your clamps moved you can hit continue.
The newer machines have the hybrid table. I created a file for making a long L bracket to register work on the bed. It also has cam clamps that are whatever thickness you want to make. I use either superglue and painters tape or the cam clamps. I do have a supplemental spoilboard that has 1/4-20 tee nuts at 2" spacing. Maybe a supplemental spoilboard sitting on top of the hybrid table would work.
Here is the file for the long L bracket and cam clamp.