There are two activities being discussed as part of world generation: terrain generation, and biome placement. In the absence of a global terrain generation override (which is what ATG is, primarily), biomes can themselves decide what their terrain should generally look like -- for instance, Extreme Hills is decidedly different terrain than, say, Plains or Ocean.
Biomes O' Plenty and Highlands only add new biomes, which is to say, they don't alter global terrain generation, so if you're hoping to get an "ATG-looking" world, you *must* choose ATG for the terrain generator. However, both BoP and Highlands register their biomes such that ATG is aware of them, and ATG will then place those biomes where they make sense in the world it generates. You can see this by looking around with WAILA and noting the fact that both BoP and Highlands plants are present, as well as by recognizing some of the more notable biome appearances (BoP's Ominous Woods biome is pretty recognizable, for instance).