I replaced vanilla spawns of creatures that were altered with your creatures, namely everything that has Rasa added to it's name like this:

NPCReplacements=(FromClassName="MegaWyvern_Character_BP_Fire_C",ToClassName="MegaWyvernRasa_Character_BP_Fire_C")

I replaced:

Jerboa_Character_BP_C with JerboaRasa_Character_BP_C
Jugbug_Oil_Character_BP_C with JugbugRasa_Oil_Character_BP_C
Jugbug_Water_Character_BP_C with JugbugRasa_Water_Character_BP_C
Manticore_Character_BP_C with ManticoreRasa_Character_BP_C
Mantis_Character_BP_C with MantisRasa_Character_BP_C
MegaWyvern_Character_BP_Fire_C with MegaWyvernRasa_Character_BP_Fire_C
Wyvern_Character_BP_Fire_C with WyvernFireRasa_Character_BP_C
Wyvern_Character_BP_Lightning_C with WyvernLightningRasa_Character_BP_C
Wyvern_Character_BP_Poison_C with WyvernPoisonRasa_Character_BP_C

I also added Spawns for others like this:

ConfigAddNPCSpawnEntriesContainer=(NPCSpawnEntriesContainerClassString="ScorchedCenter_Spawns_SouthIsland",NPCSpawnEntries=((AnEntryName="JerboaMotherRasa_Character_BP_C",EntryWeight=0.5,NPCsToSpawnStrings=("JerboaMotherRasa_Character_BP_C"))),NPCSpawnLimits=((NPCClassString="JerboaMotherRasa_Character_BP_C",MaxPercentageOfDesiredNumToAllow=0.10)))

For those Dinos:
JerboaMotherRasa_Character_BP_C
WyvernIceRasa_Character_BP_C

However now the replaced creatures do not spawn anymore at all, the Jerboa mothers don't spawn either and the wyverns only spawn when I place the shrine (which might be connected to the fact that I enabled Nests in the config which might be spawning the Wyverns near them since I yet have to see a jerboa mother or the replaced stuff with the Shrine Placed).

Did I do something wrong there with the commands?
Do your creatures need the shrine to spawn?
Does the config need to have certain settings when replacing instead of creating new spawns?
If not creating new spawns and instead replace, do I need to leave the config values default? Because they are set to -1 right now like suggested in the Spawn method discussion thread.

The creatures do spawn naturally on my Center Version but I like the features from your mod so I'd like to replace instead of making new spawns.