That's an interesting problem. I think the issue is any entities who get spawned using the biome spawner aren't saved, but I think anyone spawned by the entity spawner instead does get saved. The problem is that I don't know how to trigger entity spawner events besides when using creative mode where you can select either the biome spawner or entity spawner to spawn an entity if I'm remembering right. If you look at spawning.xml you'll see entity spawning on various days for spawning various wandering zombie hordes, and you also have POI entity spawners. I assume to have friendly animals not vanish, they'd have to be either POI or day spawned. You'll notice there is a WolfGroup and WolfPack called by the day spawners, and I swear I've seen this happen before where we got a wolf pack spawning around our den on one day and they actually were around for long enough that they helped out with the 7 day horde that came a few days later.
So, best bet would be trying to figure out how to control the day spawners to do what you wanted them to do, and as often as you wanted them to do it. I assume all of those will always be around the player, though, so you'd still want the random biome spawning friendly animals for when you're running around elsewhere.