I contacted Zero Tech Support and received the following reply:
"Please ensure you have done the following: First key on the motorcycle, ensure that you hear a click (this'll be the contactor and is normal to correct start up), have the side stand up and the Motorcycle kill switch in the off position (basically have the motorcycle in run mode). Do not apply throttle. This should take you out of storage mode."
Their reference to the kill switch is a bit vague but they mean depress the bottom of the switch. This worked for me. I recommended to Zero that they include this in a rewrite of the Owner's Manual (along with a few other recommended changes).
Just tried this, got a message that said "Motorcycle Armed" then in smaller letters,"Disarm your motorcycle to unlock App functionality"
The Storage mode message still pops up.