Welcome to the Z.
How did they correct the rear driveshaft angle, lower the transfer case with spacers?
If you're not getting any driveline vibes, and the loss in ground clearance doesn't bother you, run it like it is. If you want to make the driveline stronger and get more clearance under the belly skid, install the SYE and CV driveshaft.
Tell us about your jeep, like year, model, drivetrain, etc.
I'm curious as to why the stealership told you not to install a SYE.