Population numbers determine the number available per biome. If you embark on the border of 2 tropical shrublands, you'll have twice as many elephants available because it comes from both biomes. This does NOT change the number on-screen. CLUSTER_NUMBER is how many will appear at any time, POPULATION is the total number available per biome. For instance, the cave dragon has 2-3 per biome, I believe, and a cluster of 1. Therefore, there are 2-3 total, and they appear one at a time. If you kill one, then there' 1-2 left, and that dead one is not replaced. Setting the population to something absurd like 9,000 will cause no more to appear at any given time, but when you kill them, there's a much larger pool of animals that can still appear. Not infinite, but you'll be dead before you run out of animals. Vermin used to have this trouble, which made fishing impossible because after a few years the waters would become empty. Toady added some code that makes vermin multiply endlessly, making long-term fishing possible. I suspect that future releases will include some sort of [RENEWABLE_POP] token, so that cave dragons can still be rare and groundhogs will be able to breed and repopulate.
As for the goblin general, this is more of an entity issue. The general is basically the dungeon master, he has the job of taming the beasts and giving them to his men. When the general dies, there's no one left to make tames. You'd have to toy with the civilization tokens, I'm not sure exactly what would need to be done but I assume there's a way to do it. Ask the modding forums, they probably know. But, in my experience, mounts only cause trouble. I had elves riding grizzly bears, which sounds awesome until you realize that the bears just loitered around and my militia commander could pick fights one at a time, turning a 200 vs 1 battle into a series of leisurely duels.