Silenced deals with determinism, free will and personal identity. The lyrics question censorship and how that limits our personal reality and expression. We are therefore determined to revolt against it with our free will to ensure that we can live our lives without limits.
Trapped in the Wake of a Dream- One could argue that personal dreams (goals, not the ones when you sleep) and destiny (fatalism) go hand in hand. Chad seeks to break free from someone else's control to be free to live his life his way- more determinism, but also fatalism being transformed into free will. Also in the lyrics "Throw the chains all away, take control of your life", he motivates the listener to do the same.
Not Falling- Reflecting upon one's own being and existence. Realizing that all one needs to succeed is determinism, and that regardless of whether life is made of destiny or free will as long as one has determinism that they will get through life (see mid section's lyrics)
(Per)version of a Truth- Questioning our very existence and the world we live in. This song appears to have a negative bias (not wanting to be here), but as metaphysics involves nothingness, that seems to relate. The mentioning of daath can make this whole thing even more difficult to dissect, so I'll give you this-
en.wikipedia.org/wiki/Da%27at_(Kabbalah)Mercy, Severity- Referencing the Tree of Life, Aleister Crowley, and Yin/Yang, there is certainly plenty to be found here. This songs seems to take on a more surreal, almost sci-fi feel. This one is tricky, but you're the one in philosophy class April, so I'll leave a lot of it to you, lol. But the main thing I get from this one is that with sacrifice, one can achieve enlightenment. Seems metaphysical to me.
World So Cold- Similar to (Per)version, Chad feels like he is trapped in a dark world (existentialism and fatalism), but looks to break away at any cost to be free (compatibilism, transcendentalism too I think)
The Patient Mental- The narrator's existence is nothingness. Begging to transcend into something more. I dunno, this one is kinda vague.
Skrying- These are some of the trippiest lyrics I've ever heard, so if you can get something out of it, then congrats, cuz I got nothing, lol. But I'm sure some sort of existential meaning can be got out of it.
Solve Et Coagula- Basically the theory that the only way to achieve world peace is by there being no more humans. Hitting the restart button on life. Metaphysics to be found I'm sure.
Shadow of a Man- Questioning reality and existence by wondering whether there is another realm out there, similar to ours. On a more personal level, a person with multiple personality disorder using a secondary personality as determination to get through life. In both cases, Chad questions which is the actual reality, and suggests that maybe there isn't a primary one and that they have to be subjective to one another in order to co-exist.
12:97:24:99- This one has got a lot. Transcendentalism, destroying fatalism with free will- therefore being compatibilism, personal identity, 11:11, etc. Some of the best lyrics I've ever read. This could work as the focus of your project. The album's wikipedia page has got a good explanation of this song.
TEOATTC- Some more compatibilism involving personal transcendentalism to overcome oppressors. Some more Solve Et Coagula in here too.
Key to Nothing- Existence is nothingness in this one. Questions reality when it is picked apart and broken down piece by piece. It also implies that all of this is inevitable ("murders in the hands of motion, as it seems to be"), so there's some fate in there.
Those are all pretty basic interpretations of the songs, but you obviously know more about this stuff than I do, so you'll be able to find stuff that I can't and explain it better. But hopefully you can use some of it. And if not, it was fun to investigate and type that shit up anyways, so whatever, lol.