1. The less time they are in the store the less they will cough or sneeze in the store. Coughing or sneezing in the close conditions inside the store is much more risky than in the open air outside the store.
(a) The grocery stores where I shop all have parking garages, so ventilation in the waiting area will be imperfect.
(b) People might buy more items, fearing not being able to get back in, and therefore spend more time in the store.
(c) People will be more conscious about trying not to cough when they are in the store (and be less stressed).
(d) I don't think that the few minutes that people generally stand in line to checkout will make that much difference.
2. More room for people to keep their distances outside than in.
Any reason to think that people will maintain spacing while waiting in a long line? Especially when some will start to get nervous and worry whether they will be able to get in and if they will there be anything left on the shelves?
Did the people trying to get through the temperature screening at airports keep their spacing?
3. Fewer surfaces outside the store for people to touch or sneeze on than inside the store.
They are probably going to touch just as many surfaces inside the store plus the surfaces they touched while waiting.
4. The wait outside the store should be no longer than if everyone was allowed inside the store at once. People per minute per cash register should be the same.
(a) If the next person in line has to wait for someone to not only get through the checkout line but to completely exit the store before they can even enter, the throughput will be slower.
(b) People might panic and think that they have to get into line NOW or never get in, which could lead to more people trying to shop at the same time.
ETA:
I suppose that it depends on how strict the limit is. If it isn't as strict as requiring there to never be a wait at the checkout counters, than most of my points won't hold.