but when do you become more than a beginner and learn what the real rule is??
the "real rule" isn't a rule at all. And while I appreciate Tolak's "as much art as science" sentiment, there is plenty of science that goes into it.
To wit, some of the considerations besides just length of fish and volume of water they are in would be:
1) surface area available for gas exchange
2) the rate of the gas exchange through the surface (agitated versus calm)
3) the length of the fish is insufficient to be a good description of the waste the fish produces, a more complete list is:
3a) length, width, and height
3b) that particular species' metabolism
3c) how much that species eats and how much waste it generates
3d) the temperature of the water because in general fish in warmer water have a faster metabolism
3e) the kind of food being fed (high in protein, fat, etc.)
4) the temperature of the water will change how much gas can be dissolved in the water
5) the magnitude of the currents in the water
6) whether any of the chosen fish are going to be territorial (i.e. a territorial 5" fish may claim much much more than 5 gal as its personal area)
7) whether any of the chosen fish a shoaling and will be much more comfortable in large groups
8) whether the tank is to be planted or not, and if CO2 injection is to be used
I am sure that there are others I am forgetting, this is all I could think of quickly. Is it any wonder that 1" per gallon is only the coarsest of rules? That said, it is still an excellent excellent rule for beginners to follow. All too often people do come back from the store with 100" of fish in a 10 gallon tank -- and then none of the considerations above would matter -- that much overstocked has no chance of succeeding. Sticking to 1" per gallon at least keeps all the waste and space issues under most critical limits. It is nowhere near perfect. Even considering the above, you can take it to farcical counterexamples that obviously just wrong. 20 1" fish would probably be very happy in a 20 gallon tank (especially if they were all the same species shoaling together), but 1 20" fish has no place at all in a 20 gallon tank.
The art of all this comes from experience (either direct or learning from clubs and this forum) of combinations that have a high potential of working. The science points you in the right direction, the art is in choosing combinations that follow the "rules" and appeals to you as well!