I think I have a work -around for the Start Location issue (or more likely I dont understand it right...) :
For a Pelago map for example :
-> create a nice island with all resources needed in the Editor
-> EDIT and then ERASE the start location (but remember where you want it
)
-> Export to MapTweaker
-> Copy /paste the island (tip: where you want the copied island fill it first with ocean tiles)
-> Once both islands are nicely set, save and go back to the Editor.
-> SET both Start Locations, save as Biq and do the Player Data tweaks.
Clear enough ?