Once you select Terra Incognita there are some new options to select from, the way I select the options is that the AI will start on the old country as with the vanilla Terra map which is one of my favorites, first to get to the new world start to settle it, plenty of room for all.
The Terra Incognita map differs from the Terra in several ways, the classic Terra will have very minimal luxury resources if any on the new world, never the hard to find ones from the old country but a lot of the strategic resources.
On the Terra Incognita you get also the "good ones" on the new country, there is also fine tuning with the Terra Incognita map, by choosing it you get several new options like will there be a new world? Will some of the AI start on the new world? Which is kind of Continents for me so I tick it off. Will the old world be connected? Which I always check yes, I think it means if the old world will be in one continent or scattered a bit. In general the old world on Terra Incognita is larger then the old world on Terra for the same map size setting, which also is to my liking.
Anyways, I've tested it with G&K and so far it's beautiful, one of the best features of Terra Incognita is that the tiles are more random, not blocks of grass, plane or desert, there are some mixtures to it.
I wish the author will upload it to steams workshop.
If you read throughout this thread you will come across a Lua function contributed by ColBashar which can be added to the map and what it does is that it prohibits the map generator from connecting the old world to the poles, so there is always a free passage around the globe.
ColBashar was kind enough to post a detailed answer to my question on implementing it, since then I use it a lot.