FOWLR= fish ONLY with live rock
Reef is more of a whole ecosystem. You have light which is substituting for the sun, you have plants, animals, fish, etc...
But, mainly the main difference is in the lighting, and the chemicals. In a fish only setup, you can leave salinity lower, you can have all sorts of fluctuations in your water, and chances are, your fish aren't going to care.
In a reef you want as much light as you can stomach, and you want to keep everything as stable as possible.
Reefs usually have clean up crews, which are found on coral reefs, such as snails, hermits, etc...
Reefs usually have refugiums for denitrification and also for pod growth.
Really, ideally, a reef can ALMOST be it's own self-sustaining ecosystem. If you have good pod growth, good algae growth, and the right kind of animals, they can darn near grow and feed themselves.
Of course, husbandry is still needed...