So if you go to say a small independent pharmacy, the odds are that they'll be using one of those 2 systems? But do those systems talk to each other? It sounded like you were saying that there is just one set of rules but if you get say valium from a pharmacy on one system and vicodin from one on the other, the drug interaction won't show up - or will it? I'm not sure i understood your entire post.
Yes and no. Normal people go to "their" pharmacy for all of their prescriptions. In fact your primary care physician sends them to a specific pharmacy they don't give you a coupon to score some meds wherever you feel like. Also, the papers I get from my pharmacy list common interactions, regardless of whether they apply to you. So if something doesn't mix with alcohol it will say so.
Also, when you get a new medication a pharmacist talks to you about it.
Now if you're a pain meds junkie intentionally splitting up your prescriptions between pharmacies and doctors, and keeping each one hidden from the other then I suppose you might fool them into letting you mix prescriptions with dangerous interactions. But at that point you don't care anyway as long as you get your fix.