I prefer to do the same, actually its easier to build ingame then building ingame, exporting and importing again. However, once the map is completed we will have various tc settlements with bosses and such, the structures can be seen as improved vanilla villages, mineshafts, ruins, temples and strongholds ( the strongholds even have custom mobs ) but this doesnt holds us from making settlements by hand. The thing is with random mode when creating a infinite map it will still offer the players nice locations to explore.
It simply keep things interesting motivating peopke to explore even more esspecially because these structures will hold custom items aswell.
What im basicly doing with nlblackeagles realm is creating a huuugggeee adventure map. ( i have to say that sapphire city is a bit overdone haha )
So ye, if you'll create a infinite map it would be nearly impossibile to populate everything, thats where custom structures comes in handy to populate the empty lands