A Bakery Sando is defined less by a fixed filling than by where it comes from: the artisan bakery, the pan-ya whose case rotates a few sandwiches alongside the loaves and pastries. The premise is that the bread was baked on the premises that morning, so the sandwich is built to show it off rather than to disguise it. That puts this entry in a slightly different category from the convenience-store sando, which is engineered for shelf life and uniformity. The bakery version is engineered for the bread.
What unites the genre is craft applied to the loaf first. The bread might be a tight-crumbed shokupan, a chewy pain de campagne, a soft milk-bread roll, or a baguette with a thin crackling crust, and the filling is chosen to suit whichever loaf the baker is proud of that day. Common builds run the familiar Japanese register: egg salad whipped to a pale custard, ham and butter and a little mustard, a katsu with shredded cabbage and a brush of sauce, a fruit-and-cream sando using whatever is in season. The bind is the part bakeries take seriously. A good one keeps wet and dry components apart with a butter or mayonnaise barrier so the crumb stays intact, slices the sando cleanly so the cross-section is a deliberate picture, and wraps it before the bread has a chance to stale. A weak one lets the filling soak straight into a loaf that was the whole reason to buy it, which wastes the one thing the bakery does better than the konbini.
Because the form is a context rather than a recipe, the variations are as wide as the bakeries themselves. A French-leaning shop turns out jambon-beurre on its own baguette; a shokupan specialist builds towering fruit sandos cut to show the fruit; a boulangerie with a wood oven might press a sando on rustic sourdough. Seasonal limited runs are common, since a small bakery can change its case faster than a chain can. The high-end department-store basement version, where the sando becomes a small luxury object priced and packaged accordingly, is a distinct phenomenon and deserves its own article rather than being crowded in here.