it probably pops up from from underground tunnels refered to on the blast door map
"a rabbit has more than one hole" or something like that
also about it being cerberus, you hear three distinct sounds (the roller coaster, the dinosaur like sound, and what sounds like those ghosts from mario when it is moving) so maybe there are three different monsters that can separate and recombine that all form cerberus (which would make a pretty darn good security system)
Also, it seems like it can capture memories from people's pasts (i.e. eko's memories on the frozen frames where the cam goes through the smoke on ep 2x10) so in the last episode, those flashes we saw were all probably julia's memories that it was "scanning"
as for the reason for it not being able to get into bunches of tree, it cant pop up in there because there arent tunnels under trees (cuz of roots) but no idea why it doesnt just break into the trees