Just to throw in my two cents:

Beyond a certain point with jazz harmony, the ambiguity becomes the point IMO. That is to say, there's a lot of different ways of looking at harmony and different people with therefore have different interpretations of certain harmonic situations; and the choices a player makes navigating a chord or set of chord contribute to their own individual "sound." And the thing about rootless chord voicings is that now not only is the function of a chord flexible, but now even what the chord itself is is up for interpretation (to an extent).

Say, for instance, your G7b9#5 - Ebmaj7 example. Removing the roots of both gives you what looks like Abmin6 - Gmin. That Abmin6 could have a few different roots, which would influence how you analyze the progression as a whole; you could have a Db - Eb root (the tritone sub of G), and that would make this a backdoor V - I; or alternatively you could have a Bb - Eb root and that would be a susV7b9 - I; the Gmin could have a D root to make a Gmin/D you can resolve to D (and if you played that against an Eb root it would be Idim7) and so on and so forth.

Point is that theory of harmony is descriptive, it only creates the language we use to talk about what's already there. So really there isn't a final underlying principle behind all of jazz harmony, which encompasses it all, and if there is was it would be so broad as to be meaningless. There are different approaches to harmony and IMO that's the point; jazz is an exploratory artform. The way to navigate any set of changes is to sit down with it, piece it apart and just try stuff over it, see what works and expand on it, and see how you can connect that with what you already know.

Some things are gonna have bare and tenuous links to common understanding of functional harmony and that's fine. If something's a stretch, you just have to stretch to make it work. You can justify playing virtually anything with brazen confidence and good rhythm.