Colloquially if most people eat there, you have to ask a server for a bag its a restaurant, if its normal or at least not noteworthy to walk out (or drive thru) with a bag of food its a store. One is primarily a place to eat, and they also happen to sell food. The other is a place to get food, although you can often sit there and eat.

Internally if its a franchise most call it a store (Hi we're store #35135 and our computer is broken ...). My source is my sister who worked a long time ago at McD. So the first "site" museum is called store number 1, her job title eventually was "store manager", their annual economic results are reported as "same store sales" etc.