You can see at the very end of his email, Philip states repeatedly that he promised the Tuurnait the same as Howard had, to destroy all evidence of the mine and Shelter. He thereafter states that he is breaking his promise and types
"Kill them
Kill them all"
Thus Philip ultimately does not seem to side with the Tuurngait, endorsing their eradication by mankind(s).
For those proposing a new game in the mix, it would be an excellent opportunity for a more combative game. But on that note, I enjoyed both Penumbra (Black Plague much much more) games as they are. Guns would've taken a lot if not all thrill out of it. If I wanted to run and gun in the dark, I could always play Doom 3.
Agreed, Penumbra has brought back True Horror and Survival\Horror, my hats off to the development. I've always wanted a game just like this.
Some people complain its too short, granted, but if had even a few more hours of those puzzles I might've agreed with Clarence to off myself
Anyway, back to the point.
--------------
Philip's fate: I would imagine the Tuurngait might kill him after that stunt, or he could just wither or finely be overcome by fatigue. He never really found food since the mines in Overture. Without Clarence, Philip could commit suicide if he desired, in a whole plethora of manners that he had been avoiding
Email: I presumed it was addressed to the player as a 3rd party. He probably typed up notes from his entire expedition and merely concluded it with what he wrote at the ending. If you recall the intro, that's a hell of a way to start a story. And the game itself is a living of his Resident Evil: Macgyver experiences
Email2: Interesting reminder stated previously, only internal communications were available. I Hmm... at this. Unless perhaps the Tuurngait enabled outgoing for you. Not sure what to make of it
Tuurngait Infection: The infection is obviously pacification at the pleasantest, despite how the infected are utilized. Consider a basic human male to be a crowbar, now put that man-crowbar into the hands of a beastly man with 10 arms. The infected allow the intelligence to manipulate its environs physically, and the infected pose no threat to itself, thus the pacification. There could be an ulterior motive behind the infection, but that's the simplest surmised explanation
The Hivemind: It stands to question if the overmind is as passive as it plays off to be. True, humans are animals and would ravage such a being out of fear alone. Selfdefense is understandable. There could be a lot more to the whole thing than it was admitting to but there's nothing to speculate on
Dogs\Spiders\Worms: I presume as a result of infection, but who knows. Damn scary. That offers a quest toward whether the Overmind controlled all of them as well, and that would imply it saw Philip coming a LONG way in advance. Which might've tipped off Red's "Clarence" though Red reacted to you turning some lights on
EDIT: A thought. You're obviously still encapsulated by the hive mind when you're about to write the email. It is a possibility the email never got out and the Tuurngait sensed Philip's deception before he could carry it, which again would probably carry dire consequences
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Ending Discussion (SPOILERS, obviously)
. Also i hope your budget get a boost and that you really can establish even more , so we might get even more scared (trust me this is already the scariest game out there) but maybe some animated characters a little more monsters , animations more cut scenes etc you know abit more of the goodies