That might be worse - if the autopay amount is even a few dollars over what you put into the separate account, you'll be on the hook for an overdraft fee, which you _definitely_ won't be able to recover.
You can tell your bank to not approve overdrafts, at least in the states. They word it real weirdly at the bank, but you want to opt-out of the "overdraft protection" (the protection letting you purchase things you don't have money for).