I am an idiot.. A no start story

Yep, it will. You're only turning the Fob on or off with that switch on the fob, just saves the battery. (in the fob) I've always turned mine off when I finish riding for the day & take it inside, just what I've always done & no issues so far. I did buy a spare new fob battery to keep on the bike in case it goes flat on me while I'm out. Yeah I know I can start using the fender method but having a new battery is also easy.
 
My father always told me "When ever everything else has failed, read the instructions".
 
My dad had some choice sayings too.

"If you can't fix it with a hammer there must be something wrong with it."

"If you would just worry about yourself you'd have PLENTY to worry about!"

While driving he'd yell out the window: "Come on lady, the sign says yield, not give up and die!"

"I have a frog in my throat, must have come from the creek in my back"

Yeah, dad had some good ones.
 
So you never tested to see if the bike would start with a spare key with the brackets from the panniers on? I'd test it out to make sure you can get close enough to the location to start the bike incase tou ever do need to do it that way.
 
Assume you also keep that Allen key needed to open that fob up