Back around the time the
Exposure album was released Robert Fripp was writing a column for Musician Magazine, and in one column he described the middle part of "Breathless" as being "without meter". He claimed it consisted of an undifferentiated stream of 30-something 8th notes, repeated at three different pitch levels.
I find that description disingenuous.
To my ear the middle part very obviously alternates between two measures of 11/8 and one measure of 7/4. The bass & drums very clearly articulate this. I suspect the feeling of 3 you're hearing comes from the guitar part, which is playing repeating phrases of 18 eighth-notes; and yes 18 is divisible by 3, but the "undifferentiated stream" aspect of the phrase(s) makes me think that we shouldn't be inferring any barlines from the guitar part.
Anyway, if I were tasked with transcribing this tune I would bar the middle section as 11/8 (subdivided 2+2+2+2+3) x2 followed by 7/4, and then for the guitar part I'd beam all the 8th notes in groups of
four (regardless of how the beams crossed barlines) and then put a large phrase marking (like a slur) over groups of 18.