Basically through both the gamedata blueprint and the gamemode blueprint you can force the game to use alternatives to the base game and then still load a different map such as TheIsland. Open up the two blueprints in the GenericMod found inside the Content/Mods folder and look at what all defaults you can change. I am not entirely certain what all is entailed with Remapping NPCs since the DinoEntries are seperate from the Remap NPC default, but as far as I understand it needs only to be within the scope of the UE4 engine (which is a pretty wide scope).
Regarding your second question, you will just need to leave existing dinos alone in the PrimalGameData blueprint since they all correctly reference the games normal assets provided by the dev kit unless you wish to replace the said dino. For example, if you want to replace say the Dodo with maybe a DodoRex, you would change Dino Entry 0 in PrimalGameData_BP to your new blueprint, but leave entries 1-27 alone.
Hope that answers your questions, otherwise maybe with something more specific Drake can show you the way 