Generally, "in" is more specific. "At" is more general. I saw him at the store. - Maybe inside the store. Maybe outside the store. Maybe on the store's roof. ;) I saw him in the store. - INSIDE the store only. There are occasional phrases that require "in" or "at." These, you just have to remember. When I think of constant examples, I'll let you know.

no, they are similar but different. Both "work in a shop " and " work at a shop" would still be understood. However, "work in a shop" gives a more precise location where you work (that is INSIDE the shop). Whereas " work at a shop" can be broad, you can either be just visiting that place when you work or any doing any work for the shop (outside or inside)