If I reroll maps but not terrain on this, MekHQ will still generate maps with mostly little terrain and mostly flat correct? If so, reroll terrain.
Your assertion is correct. "Terrain" indicates the general type of terrain generated, while "maps" indicate a very limited number of terrain types chosen from. The easiest way to detail it is using Urban Terrain as the example. Getting Urban Terrain vs Savannah terrain means that you know you're going to have a fair number of buildings on the map. Then, inside "Urban", you have Town Ruins, Light Urban, Heavy Urban, Urban Fortress, and a few others.
Speaking of which:
You have one reroll remaining. Flatlands stayed the same, but because it was rerolled it generated a new map within the Flatlands tables, which is the "generic town." I've never seen that result before, so I went ahead and loaded it into the MegaMek client. Based on what MM was showing me, the easternmost maps for your game will be low-CF Urban mapsheets (so, no Skyscraper or Heavy Urban, but Suburban or CityTech with Light and Medium Building counters on it, are both possibilities).