How come heating milk in the microwave is safe

Are these bacteria also present in sterilized milk?

If something is sterile, then by definition it does not have any live bacteria in it. That only applies while the milk is sealed in its original sterile container, though.

Can these bacteria be introduced from the air or from the bread [flour]?

Absolutely. There are bacteria and yeast living in the air, flour, and on every surface in your kitchen (including your bread maker). Wild yeast and bacteria in the air and flour are used to make traditional sourdough bread.

Are there other bacteria or toxins that will develop in sterilized milk when exposed to room temperature for a few hours?

I'm not sure how this differs from the above question, so: yes.

Speaking practically, if you are setting the timer for less than 4 hours, I think the risk of getting some sort of illness from this is rather low. The baking process will likely kill the bacteria before they have a chance to produce enough nasty toxins to make you sick. If you refrigerate the milk beforehand, you can even buy yourself a little extra time, since the milk would need to warm up slightly before bacteria could start reproducing in it. I still wouldn't make a habit of this, since there is still some risk of contamination. Leaving milk out on the counter just isn't a good idea, even if it was originally sterile.

It's not the sugar that caused the milk to curdle, it's the milk itself. Dulce de leche and caramel are both usually made with either cream, condensed, or evaporated milk. The issue with regular milk (especially skim), is that it has such a high water content and low fat content. The fat in cream buffers the protein, helping to prevent curdling, and the canned milks have already had most of the water removed, making them less likely to curdle.

The sugar could also have a buffering effect on the milk protein, unfortunately you have a catch 22. In order to buffer the milk form curdling, the sugar would have to be dissolved in the milk. In order to dissolve sugar in the milk at a 1:1 ratio, the milk would have to be heated past the point where it would curdle.

You might be able to prevent this by using a double boiler until the milk has reduced a lot. Making a caramel requires almost all of the water to be cooked out of your syrup, so this will take a really long time and isn't advisable.