To me they're doing their best Metallica meets Pantera played by Dream Theater on Train of Thought, and to me I don't see it as dark or cold, but aggressive and energetic, the riffs on ToT... JP is the riff master on that album compared to Mangini era JP. I always think of the basic chugga chugga main riff of The Enemy Inside as the most stock riff of modern DT. Which is why I'm surprised at his new album and the new LTE single, he's still got that in him. Jordan's keys over the last few albums also sound more serious, and dark, than in the 00s.
As for Awake, aside from The Mirror which is really just aggressive, I don't find the darker moments dark, as much as sad. They have a sad, longing feeling to them, it's in the keys. The album, along with IaW, is also of its time, that post-80s, early-mid 90s feel that is present in most popular music of the time period (early/mid 80s-1994). I don't feel that from modern DT albums, for the most part. The only dark song they did prior to Systematic Chaos is Disappear.
BTW this is all based on the music. I don't really put too much weight on lyrical content in DT's music, and I also don't find DT's music very dark relative to other music out there.