Thanks, TheFuzzyTie! I really appreciate what you are doing for me here. It feels like I'm finally getting at the answers that have been eluding me for quite a while.
Coming back to the questions I raised, I had the following on mind when I asked if the verb "work" had anything to do with the selection of prepositions before place-nouns. That is, to my innate English grammar (which seems obviously not in sync with that of the natives:lol

either prepositions sounded OK in the following examples.
I had dinner at/in the restaurant.
I bought it at/in the supermarket.
Does the verb "work" (work at, not in) have something to do with it or am I just wrong again?
And yet you sounded as if to say that we don't really use
in in constructions like
He works at/in MacDonald.
To tell you the truth, the only one of these that you really couldn't say would be "in," and slightly "with."
However, after reading your second batch of explanation, I came to realize that when describing activity it would be better to use the preposition
at rather than
in before place-nouns or building-nouns unless you wanted to emphasize something was inside or within boundaries of some sort. Am I on the right track? Following your logic, if I'm right, it would be better then to say "She works at a shop" rather than "She works in a shop. On the other hand, it would be more natural to say "There are seven tables in the shop" rather than "at the shop." But then, "There are seven tables at the shop" sounds a little off but "She works in a shop" doesn't sound so bad, don't you agree?
By the way, relating
activity with the preposition
at led me to an yet another question. Questions spring eternal. ;-) I don't know if you are following
24, the Jack Bouer series but I do.

In recent episode, Jack the hero goes against US president to expose her attempted cover-up of Russia's involvement with terrorists against a peace treaty. Chloe, the faithful friend of Jack, who is in charge of the New York branch, doesn't want to see him injured or dead so she orders her staff to locate Jack in order to bring him in safe. And one of the staff says, "I'm on it!"
To me, the distinction between
I'm on it and
I'm at it is not so clear, and if there's any, I'm not sure if they are right either. So I think it would be better to blurt out what's in my mind and hope that you would sort them out for me. ;-)
At seems to be used in order to express that someone is doing something, so if I say "while we are at it" it seems to imply that
while we are doing(dealing with) one thing, why not do another related thing. And "Keep at it" sounds to me "Keep at what you're doing, continue, carry on that sort of thing.
ON reminds me of "concerning" and "trying to make something work better". So if I say I'm on it, I mean that I am working (or will work) on it. "You are on it, too?" sounds like either "Are you working on it?, Are you part of it as well?" or "You too know about this?" And when using
on some sort of selection seems to be involved as well, when I say "He's on the team." or "you are on!" So when the above staff in the episode says "I'm on it" seems to imply that he appoints himself or volunteers to take care of the problem. I hope I'm not completely wrong. Thanks in advance and have a nice weekend!
Oh, one more thing with
with.

If someone says, "He's with ABC law firm," it implies that he is a lawyer not a paralegal or the lowly staff? And if a cleaning staff in the FBI claims that he is with the Bureau it would be downright wrong, wouldn't it?