As far as I can tell, yes you're exactly right about the way they work in practice. I think the key difference is in the variables Shuffle describes the maps as generating such as world age and rainfall, as I think these are identical across the vanilla preset maps (so an archipelago map can have varying sizes and numbers of landmasses, but all will be essentially temperate, 4-billion-year-old worlds, and so with similar numbers of mountains, and ratios of plains to grassland or forest).
As I say, though, I don't find this makes a clearly detectable difference in practice. There also doesn't seem to be a temperature variable as in past Civ games: your worlds will always have a polar region grading latitudinally into a jungle zone, with similar arrangements of intervening terrain types - you don't get cold worlds with disproportionate amounts of tundra, or hot desert worlds with little or none.