With 'luxury' resources(as opposed to food) I generally find they do clump although once in a while one will show up far separated from the others. I haven't noticed any particular problems with realism there, myself. Really wheat doesnt all grow in one place, nor did it in ancient times, wheat or related grains grow all over the place, different game animals / potentially domestic animals, same thing. Some things are limited by range (usually the more limited the more expensive and "luxury") but the sort of things man considers food staples, not so much. (although, I would think one region of the world would tend to have wheat in it, and another rice, for example. But region there means an area much larger than most civs would have to themselves.)
As far as game play realistically spread food staples may be less interesting rather than more.