Yeah, it will be the Biome only, not the mycelium. Much like how ME^4 has the entire complex be Mooshroom Island except the spatial area which is plains, that way the only place mobs can spawn is in the spatial area. In my case it will simply be shielding a very small area so the player can hide. Then plains over the rest, except...well, except. 
There will be very tough monsters out there. Much like Crash Landing venturing too far from base without preparation will kill you. Unlike Crash Landing your starting area will be fairly large and actually lit up so you aren't in immediate danger. Of course, between the needs of a Tier 6 Blood altar, a full Thaumian workshop and all the Botania goodies you'll need to spread out much further than Crash Landing's more compact setup.