Most of your answers are in gamestages.xml, but I'll see what I can elaborate on:
So the group names are just that, group names that can be edited and whatnot. The loot ones use the zombie lists that are in the SleeperGSList from entitygroups, and I find it weird that they're named "loot" when they have nothing to do with loot.
So let's look at S_Default_XS, here are the comments in the xml:
1. emptyChance: the chance of the entire sleeper VOLUME having no zombies
2. count: after emptyChance has been checked, the total number of SLEEPERS spawned is determined by the count
3. decoyChance: determines how many OF the spawned sleepers will be DECOYS
4. decoy1hpChance: determines how many OF the spawned decoys will be ONE HIT POINT DECOYS
Full hit point decoys: Will never wake up due to sight/sound events. Will wake up if attacked.
1 HP decoys: Will never wake up due to sight/sound events. Will die instantly if attacked.
That should help with that.
You can make a custom sleeper group in the xml to call from, so yes you can have your bear; just edit the prefab xml to point to it. My ranger station has a nice beary surprise. =)
The gamestage adjustment really only affects WHICH actual zombies can spawn from the SleeperGSList, so that if you enter say, the pharma building at level 1 you probably won't get radiated spiders in those harder areas, because you'll be at a GS 0, so even if the modifier is "hard" you'll only get an additional 500, making your GS in that area 500, which gives you a football player, skateboarder, steve and a nurse.
Hope the info helps.