So in light of Jaelis crucial information, I have studied again the questlines listed in wikia, also paying more attention to the description texts, and noting which provinces are north/south and who owns them, what the quest are asking and the storyline they are giving, and I think the whole thing now makes a lot more sense. Understanding the context and the story line definitely helps. So I was also able to figure out where other alternative quest versions should exist (not listed in wikia, because the people who contributed there did not happen to get those versions).
Also it seems versions where one conquers the North provinces tend to be the ones missing. And looking at the map, I can see an explanation: once Okahe is conquered, the next options are New Cragshire (loot reward) or Desperation (expansion). So makes sense more people would go for the expansion. (ie start conquering the South).
So now my working my working hypothesis is that the bonus questline kicks in once all the main IndA provinces are acquired. So if Garrincton is acquired last, it will trigger the bonus quest. But if it not acquired last, then the bonus quest will not kick in when it is acquired (as per Jaelis experience). And looking at the logic & patterns of the questline, I am quite confident that one can do the same by approaching from the south route.
So options for getting to Garrincton (which seems to be needed to make the bonus areas scoutable) are:
from the North: Okahe->New Cragshire->Rantford->St Marque-> Garrincton
or from the south: Okahe->Desperation->Las Penas->Dragon city-> Garrincton
or from both simultaneously (ie conquering both North and South provinces).
And indeed Myciena's quesltine guides one through the above options.(One can do the IndA map while the main story quest is still of an earlier age, but I will follow Myciena's main questline. From all the quests listed, it seems can be completed while in CA which is good news for me
So my conclusion is that to obtain Garrincton and avoid the bonus questline, one should not leave it for last, but follow the north or south route. And if one wants to do the main story line quests at the same time, then avoid acquiring any of the provinces of the 'other side', because then the quest options will be affected. So in this case only conquer 'North' provinces OR only 'south' ones, but not a mixture of both (not until Garrincton has been acquired). Also provinces should not be done purely by negotiation, because then Myciena will be asking you to acquire both south and north provinces, rather than giving the option to stick to one route.