When The Noose originated, there was a lot of political punk/hippie genre focus on APC, especially their song Counting Bodies... and their album eMOTIVe. At the time, we were moving hard against Iraq under G.W. who appeared to be a focal point for APC back then. I always felt The Noose was written for him. By and Down, to me, does not seem connected. I think that we all perceive lyrics with music differently based on the loose and suggestive subject matter of the music as a whole. I also think that we automatically connect it to things occurring in and around our lives when the music surfaces. I believe that this is the reason we can listen to Cat Stevens or Led Zeppelin and still enjoy it today, all the while conceiving emotions associated with events in our interpersonal lives and exterior lives at the time we first heard the music. Led Zeppelin will always remind me of Fast Times at Ridgemont High and many, many other things. Of course, Tool's No Quarter takes things to a whole new level (a basement or dark room where some kind of evil resides); that evil in the basement or in the dark room down the hall is different for us all, but absolutely nothing like Zeppelin's No Quarter.
I think that By and Down has something to do with a female or at least a person of sexual affection (I say this in consideration of the differences in people's sexual orientation). I often ponder what the band is feeling or thinking about the song for only they really know. Maynard loves to keep people guessing and pondering; it is his true signature trait. He loves to be elusive. He seems to enjoy writing music that is vaguely familiar so that anyone listening can connect it to any thing, event, or person to which/whom it seems to pertain for the listener. If he explained its true roots, it might not appeal to so many; it might simply become irrelavent to the listener. I say this as I have found this to be the case with many songs by other bands that started off great until I read the lyrics.
Ever listen to The Cocteau Twins? Liz often has no idea what she is even singing about; it makes for some good mind pondering. She reminds me of Maynard in that way. She is elusive as well.
By and Down to me reminds me of the character, Jenny, from Forest Gump, only in the case of By and Down, Forest is some average person without a mental deficit and is struggling with his perception of Jenny as she becomes self-indulging in alcohol, sex, and drugs; non-chalant towards Forest's dedication and true love for her; and to her taking advantage of him before dying (leaving him alone and betrayed) of her own self-destructive nurturing. This is applicable on so many levels and for so many people; like the guy who CAN have the girl (for a price), all the while questioning her motives and morals and becoming completely distraught while loving and hating her at the same time before realizing that as a matter of consequence he CANNOT truly have her. The Noose seems to be about one's destruction of large masses and one's pondering of how that person lives with him/herself while By and Down seems to be about one person's self-destructive self-indulgence and one's pondering of his/her own perception of that person. Just some thoughts.
None of this is to say that I do not appreciate your point of view; rather, I simply find the topic interesting and good for a multi-faceted conversation.