The best I can figure out--and I may be completely wrong--is that these "Habano" varieties are descended from the seed originally smuggled out of Cuba at the start of the embargo. Commonly grown varieties in Cuba at that time were mostly derived from the original Corojo, and possibly Criollo, which replaced, in succession, the slap-dash "Vuelta Abajo" varietal mix, due to disease issues. Whatever it started out being, it has been cultivated in Central America for a half century now, and has very likely experienced some minor crossing with various local varieties. That is to say, "Habano" from Honduras and Nicaragua are not only different from one another, but are probably not the pristine original (of whatever it was). The contribution of slightly different soils, and different cultural practices does make some difference, but there is no way to tell how much.
I have seed for the original Cuban corojo (mislabeled by GRIN as "Coroja") and the original Cuban criollo, also from GRIN. They make excellent cigar leaf, but neither is a dead ringer for Honduran or Nicaraguan "Habano". Besides, the Corojo 99 is even better, and is nearly twice as productive.
Bob
EDIT: So...I don't know how you might obtain seed from Nicaragua or Honduras for their "Habano" varieties.