That's almost it. I just finish playing the game, and rewatched some sequences from the end of BP too. we have to pay a lot of attention to what is beeing said and connect the dots. If you do this you'll see that in the end it comes down to this:
Dr.Swanson said it was possible the cure wouldn't work entirely, and it DIDN'T. It was not expected that clarence would get tranferred to another body, and although he got rid of clarence, he remained under the hive's influence.
In the last stage of BP (phillip wakes up in the examination room), the light effects, the vanishing walls, the vanishing books, were references on the hive's desire to erase all evidence of the place and itself. It is talking to him and influencing his mind, scaring him, trying to get him to do what it wants.
After sending the email, the hivemind started messing even more with his head, and Requiem started. Requiem is all inside Philip's mind and it is all about Phillip trying to escape the influence of the hive that is trying to trap him. (requiem is all about escaping areas)
Phillip sended an email betrying the hive, but even if he didn't, it wouldn't change a thing, because Phillip never gets out of the facility: There never was any intention from the Hivemind to let him go. The only thing it promissed was to tell him what he had told Howard (its origins). The Hive couldn't take the chance of letting him go, and moreover it instructed phillip (during the tests) that one has to sacrifice oneself for the good of the group.
Also the hive asked him to send word for someone ELSE to destroy the evidences, it didn't ask him to destroy the evidences himself when he arrived home
Phillip knew he woudn't ever get out, that's why he wrote in the email "if we're lucky, by the time you read this I'll be dead" because if he wasn't dead, he would be infected.
During Requiem and specially at the end, in Red's room, pay attention to what he says and you'll understand that there is no escape from that situation. The only way out is by entering the incinerator. althought it is all in his mind, entering the incinerator means phillip managed to fight the hive's influence and just "turned his brain off", dying. - By choosing to exit through the door makes him go to the boat, and you think he escaped but he didn't. if you look closely, its not the real boat, its the boat from the illusion in his mind, and he can't leave, he's trapped, and soon after there's a white flash, and all that means his mind was completely taken over by the hive.
the hole time from the end of BP to the end of Requiem he is lying on the floor of examination room, and the "good" end is the incinerator, so he dies, escapping the take over from the hive.
If you pay attention to the speeches during requiem will you find clues to all of this. for instance there a part where the Dr.Eminiss says that if someone would find the entrance to that place they would never find the exit.
Excelent story and closure.
Oh and one more thing, the email at the start of each game doesn't mean YOU or anyone else is receiving the email. It is just that thing they like to do in the movies: to put a part of the end in the beginning to make you curious about how the situation got to that point.
If you liked my post, send me a PM!