Baked food and Bacilus Cereus

One of the largest misconceptions in food safety is that safe food does not have bacteria. Safe food is, like all other food, always contaminated with bacteria. The difference is that safe food has been kept under conditions which have not allowed the bacteria to grow to dangerous levels.

Cooking and baking both kills some bacteria, but does not sterilize the food. And even if it did, it gets recontaminated immediately anyway (exception: canned food in airtight containers). The difference in shelf stable food and perishable food is not that shelf stable food has no bacteria, it is that shelf stable food does not grow bacteria at room temperature.

The items which you listed - bread, pies, etc. - simply don't have enough moisture to sustain a bacterial colony. This is what makes them shelf stable. Other shelf-stable foods are preserved in other ways, for example some kinds of pickle contain enough acid that bacteria cannot multiply in them. But there is nothing inherent in baking as a heating method that creates this result. If you fry some dough into a donut, it is also shelf stable. If you bake a casserole, it is not shelf stable and needs refrigeration. Depending on what you put in it, it will develop some pathogenic colonies if left outside, with B. Cereus a common possibility.

If you want to think about food safety, you always have to think in terms of "which factor necessary for bacterial growth am I missing in this food". This is what prevents the most frequent misconceptions which people automatically come up with when starting from other assumptions.

No. The difference is the food itself, not the cooking method.

"Cooking" is a general term that includes baking, frying, roasting, sauteing, boiling, steaming... etc. "Baked" foods are cooked.

You could hardly expect to leave a lasagna out on the counter (a baked food) without it developing dangerous levels of bacteria. Same thing with something like a cheesecake or cakes with perishable frostings like buttercream or whipped cream.

Bread, particularly, simply isn't a welcoming place for this bacteria - it's dry... From the abstract of an article from the Journal of Applied Microbiology:

Bread doughs were artificially inoculated with spores of six Bacillus cereus strains at different inoculum levels and counts of survivors in bread determined during storage at 27·5°C. No B. cereus were isolated from the centre crumb of 400 g loaves when the dough contained less than 104 spores/g whereas with 800 g loaves survival occurred with doughs containing 5·0 times 103 spores/g. With all strains there was a period of at least 24 h before multiplication took place in the bread. The inclusion in dough of 0·2% of calcium propionate, based on flour, effectively delayed germination and subsequent multiplication of B. cereus spores. It is concluded that the risk of food poisoning due to the presence of B. cereus in bread is minimal.

So, no, you can't "bake" something and expect it to be magically shelf stable.