In the Unknown Container chapter, in the Chopin example, would you really have the performer actually perform this as if it were written q / q q // q' q / q q // q' q / q q // q' q / q q // q' ? If so, I'm afraid I think you're dead wrong on this one. I don't know this piece, so I went to it afresh, with your analysis in hand. Sure, it can be played the way you suggest, but that would be a very pedestrian, boring travesty of what the bar lines clearly indicate actually say. If it's performed as written, it has a totally different, far more interesting character than as you divide it up. This to me clearly suggests that the notes alone, analyzed without bar lines, accents or other indications of the prosody desired by the composer, don't tell the whole story as to how music should be performed.

     It seems that you use bar-lines to indicate performance variations of volume and tempo. (a) When the first 4 s are placed between bar-lines, on beats 1-2-3-4, they are in rebound grouping with the maximum volume on the first and the others gradually softer and possibly slower (as in the word "dictionary", or the second bar of Over The Rainbow). (b) When a bar-line is placed between the third and fourth s, on beats 2-3-4/1, they are in pick-up grouping with the minimum volume on the first and the others gradually louder and possibly longer (as in the word "mid afternoon", or the first 4 notes of Oh, When The Saints).
     In the Unknown Container chapter, bar-lines are meant to indicate the rhythmic structure of Beats and Off-beats (with their Alternation), that are fixed and not variable (as are volume and tempo). A performer may either vary volume and tempo to (a) correspond with the rhythmic structure and thus draw attention to it, or (b) contradict the rhythmic structure and thus draw attention away from it. Both procedures are artistically possible and the contradiction often creates situations of subtle and pleasant ambiguity. These choices seem to be an integral part of the unity/contrast equilibrium which every artist (both creator and performer) must strive to achieve.
     In order to avoid the confusion of this dual usage of bar-lines, we strongly recommend that they be used exclusively for the rhythmic structure of Beats and Off-beats and that the traditional Italian terms (and abbreviations) be used for variations of volume and tempo (in this case "calando" for the first 4 s and "simile" for the following group). It would then be possible to continue this discussion with greater clarity and precision.

     But looking at the Chopin example, the default prosody for performing 4/4 music is 1 4 2 3 | 1 4 2 3 | etc. where 1 is stronger than 2, 2 stronger than 3, etc. I learned this by hard experience when I wrote software to generate a midi file.
     At first it was all monotone and horrible. As I experimented with the prosody, I eventually came up with a formula that sounds like a decent human musician (with perfect control of the sostenuto pedal) is playing (I think).
     So, back to the Chopin, the notation as is suggests how it should be performed, prosody-wise. If you change the placement of the bar lines, then the default prosody is fouled up, and you'd have to find a way to notate the 1 4 2 3 pattern. Not a pretty sight.
     I think it's far more important for the notation to reveal simply how the prosody is supposed to go than to reveal the harmonic rhythm. The interesting thing in this piece is that the two are out of phase. Analysis can reveal the harmonic rhythm from the existing notation, but if you change the notation to make the harmonic rhythm explicit, there is no way in hell without explicitly notation that one could know what the composer's intended prosody is.

     Most would agree that performance often requires appropriate notation. Rhythmic and harmonic structure are integral parts of the information to be noted. Even more so, when prosody and rhythmic structure differ, as knowing this (what they are and how they differ), is power to better understand, feel and render the music. Hopefully, the performer does not also have to do a detailed composition analysis to figure it out, as this is why we have notation.
     Considering that prosody and dynamics already have a rich notation, that rhythmic structure notation only requires bar lines, that performance accentuation and dressing does not exclude fundamental rhythmic and harmonic structure, and that MusicNovatory strives for clarity and true understanding of the Music phenomenon, you may have to adapt, as you go through this document.
     Still, these questions are interesting and considering them can provide valuable insight and knowledge, especially on the role of proper notation and clear logical definitions, to limit confusion and favor understanding.

I was most interested by your rhythmical analysis of the Bach fugue. I can only agree with you 100%, it is so much clearer this way. I had never noticed this before.

You have no idea how precious your comments are, especially in a case like this where a change is suggested to such a revered work. Many, many thanks.