Land connectivity has zero impact on conversion. Map differences are the reason why some aspects are lost. If 3 ck2 provinces map to a single EU4 one, then the guy with mods development/buildings among those 3 gets to be the owner of the EU4 province. Same for reverse - if a ck2 province maps to 3 EU4 ones, then the owner gets all three.
If an owner holds multiple titles of same level as his primary title and is in christian world, the primary one is his main title, others split and become junior partners. For duchies, he'd have to be King to avoid this.
We don't map appanages. They were introduced as an EU4 concept/mechanics relatively recently, while this converter is old and I have no intention of expanding it further. If you wish appanages, change the vassals to appanages and give the owner the french government form that allows for them.
Also, feel free to edit whatever country you disagree with. We assign "Chartered Monarchy" to those countries that have a very large amount of laws (limiting sovereign rule), akin to RL England of the time.