is a commercial unit allowed to tap into the existing water supply system of the residential section?

In most cities this should not be a problem. The commercial user will require a backflow valve, even if the residential users are not required to have one.

the water utility is in charge of that, you aren't

Sounds like it depends what has been written in the rules of a water district and the commercial guys write things like they want it. Because the developers are all commercial, even if they are selling residential. At the time of the agreement, there werer no "residential" interests, and certainly no one on the water board. Now, there is only 1 water system in the ground and it is for everyone, even the fire hydrants. Unless there is something unusual like a commercial unit with a huge water demand that would justify its own pipe from a different main. As for doing it, it is an engineering issue of the development of the project, size of pipes, flow demand, expansion of the system, expansion of development, etc. Go talk to whoever is responsible for the water system and ask questions regarding your water supply.