You first have to be the mayor of a town, then it's a few simple commands.
/town set perm off
The command above stops everybody from building, destroying, using items or using switches anywhere except their own plot (except the mayor and I am not sure but I think the assistant).
You can also enable/disable individual permissions (build, destroy, item or ...
Yes there is. I haven't read the Towny docs for a while now, but you can set up mayor/assistant/resident permissions using the in game commands.
This will allow you to choose exactly who builds where, set mob spawns/fire spread/explosions/pvp... it goes on.
The best way to learn it is play with it yourself.
Try something like /mayor help and just keep ...
I had a quick look over the documentation and I couldn't find away to do so. You could either request that as a feature here or you could use WorldGuard to make regions around the towns, Then set flags so only the people you specify (or groups) are allowed into the area.
If you need more help with the second option - PM me on the Bukkit Forums (shadrxninga)...
No, spawn rates will not go down. However, if you place the spawners on land that isn't flattened, then that might affect the spawning rate. You should set the spawners at least 1 or two blocks away, although right next to another works too.
Yes, WorldGuard should work fine for protecting areas from towns.
I'll assume you already know how to use WorldGuard. If you are not familiar with it, go through the basics over at the WorldGuard Wiki.
Create a region so it surrounds the area you want to protect. Note the region id.
Type "/region flag [region id] blocked-cmds plot, town, nation"