As the grate is porcelain coated cast-iron, I wouldn't recommend cutting it. I found it fits nicely on top of the existing grate and used it that way a couple of times as an experiment.
It's not uncommon for customer service to tell you to only use their product the way they intended. There are liability reasons for this. Sometimes they're right, other times they're being overly cautious. For example, most manufacturers will tell you to only use their own brand accessory parts when, in reality, any manufacturer's accessory parts will do (for example, the hose that lets you hook up the Weber Q to a 20lb tank).
I suspect if you were to ask Weber if it's okay to use a flower pot base or a Brinkmann charcoal pan in the WSM you'd get a similar response. I know they would tell you not to drill a thermometer hole in a Weber Grill.
So experiment at your own risk.
Bill