You have the right idea where it comes to NI maps.
This mod works by sprinkling magic sites around the map. It has 45 new magic sites, which add independents back randomly into the game. Some of them are found automatically when you take a province, but most require site searching. This was an intentional design decision to make them more rare and special. Half or more of the sites also have a small gem income attached to them. Most of the indies in this mod are standard, but there are some that are not quite so standard.
Here's a few examples of non-standard indies:
#newsite 770
#name "Hoburg Workshop"
#path 3
#level 2
#rarity 1
#loc 735 -- any land
#res 25
#mon 982 --clockwork horror
#gems 3 1 --earth
#end
#newsite 761
#name "Pirate Cove"
#level 0
#rarity 0
#loc 64 --coast
#mon 871 --pirate
#com 870 --captain
#gold 20
#end
#newsite 765
#name "Black Lotus Clan"
#path 5
#level 1
#rarity 2
#loc 17119 -- any land unique
#com 1257 --ninja
#gems 6 1 --nature
#end
Typical indies like bear tribe warriors and lizardmen are also represented in the mod, and most of the non-standard ones are rather more rare than the standard indy types. There's not really an era consideration given to the mod, it was made fairly generic to be able to fit in all eras without being too strange. That said there are a few sites that don't completely conform.
There might be some interest in generating maps how you describe, but that would be a somewhat different project than this one, and probably more difficult
.