You are right, that's what a lot of the responses were from reddit and I went with it when I see Ben's response because that's referencing Toumas' songs, which are in a way, his words.
We tend to think that because the artist has a lot of resources, that absolutely nothing could possibly be missed or not be exactly what the artist intended or that what the artist intended always has to be more than "it sounded cool."
Kick drums too high on Systematic Chaos? They thought it sounded cool.
Weird vocal glitch on "people just don't have the time for music anymore"? Likely something they just missed.
Floor being too low on the chorus (I think it's the chorus)? Either they didn't notice or they thought it sounded cool.
Missing beat right before the solo to Stairway to Heaven? Just how they happened to play it that day.
Doesn't usually mean much more than that, though sometimes it does. But people, many of us, are creative and you can always....ALWAYS...come up with a story to justify whatever you want.
Kick drums too high on Systematic Chaos? They represent the furiosity and sense of attack of the characters in the songs.
Weird vocal glitch on The Astonishing? A commentary on artificial artifacts on modern music and the impact it has on people's attention spans.
Floor being too low on the chorus? A commentary on our relationship between music and vocals and reliance on vocals in modern music.
Missing beat before solo in Stairway to Heaven? Commentary about people rushing to get to the rewards in life.
It's easy, and usually meaningless.