Think of the FC as mostly measuring the chlorine capacity or that held in reserve, but only the amount of chlorine that isn't bound to CYA (and is the more potent of two forms -- namely, hypochlorous acid) is "active" or powerful. Think of an army of soldiers where only those on the front line are "active" and have guns. The fact that you've got many more soldiers in reserve not fighting is irrelevant in terms of how quickly the soldiers kill the enemy. The reserve only tells you how long you can continue to fight when "active" soldiers die killing the enemy and get replaced from the reserve.
The shock levels of chlorine where the FC is around 40% of the CYA level are technically equivalent in "active" chlorine concentration to that found in 0.6 ppm FC with no CYA. The "active" chlorine concentration is not only what kills bacteria, viruses and algae, but is also what oxidizes swimsuits, skin and hair. My wife experiences this effect every year when she swims in an indoor community center pool over the winter that has 1-2 ppm FC with no CYA and her swimsuits degrade (elasticity gets shot) every season so she has to get new suits; also, her skin is flakier and hair frizzier. In our own outdoor pool with 3-4 ppm FC and 30 ppm CYA, the swimsuits have lasted for many summer seasons with no degradation and her skin and hair are far less affected. The difference is that our pool with CYA is equivalent to 0.1 ppm FC with no CYA so the indoor pool has 10-20 times the active chlorine concentration and is degrading her swimsuits, skin and hair 10-20 times faster than in our outdoor pool.
There IS an affect on human health with FC alone regardless of CYA level and that is if you were to drink the pool water. In this case, it is the chlorine capacity that is more relevant than its reaction rate. This is because there are lots of compounds to react with in saliva and in the body and plenty of time to do so. The CYA may slow down these reactions, but they keep on occurring and the water is in your system long enough that it is the FC or total capacity of chlorine that is relevant in terms of how many chlorine by-products your body will eventually get exposed to (though technically some by-products are formed more when the active chlorine is higher). Even so, the EPA rule of 4 ppm FC being a limit in drinking water is for drinking many quarts of water EVERY DAY. You aren't normally drinking very much pool water, even if you accidentally took a gulp.
There is some dermal absorption of pool water, but what I can find it's relatively low and the chlorine tends to react with the skin surface before it gets in any deeper, though technically having no CYA would use up the chlorine more quickly before it got too far. It's hotter water as in showers and spas that have the pores opened up more and it's also when there's more water (and its contents) that are inhaled. Even so, this shower issue is subject to debate and there haven't been studies correlating ill effects. Also, using CYA will reduce the outgassing of chlorine as well as the production of the most volatile disinfection by-products (e.g. nitrogen trichloride). Virtually all of the respiratory and ocular problems associated with pools are indoors and I suspect without CYA.
Richard
This has really helped my understanding of the process and has helped me understand the CYA/Chlorine chart versus just understanding how to use it. Is there a place on the web site where the "Pool Water Chemistry" link is saved?