Nothing canon about this, but my personal head canon says they're on opposite spectrums.
The Resonance Realms is on one hand, followed by the Matrix, then in the middle is the physical meat world, then off to the Astral, then all the way on the other hand is the Meta Planes.
Resonance and Magic are just too far removed and can't even perceive each other's existence.
My headcanon is almost the opposite. We know that magic comes from mysterious forces that flows through people and is shaped by their thoughts, and that it's not just their conscious thoughts either. There's a lot of suggestions that it's also shaped by the collective unconsciousness of all of metahumanity, in things like the metaplane design, spirits often appearing as metahumans, etc.
I think the Resonance is the product of the same or a similar force being shaped by the Matrix's collective unconscious instead of metahumanity's. That's why it's a sort of funhouse mirror reflection of magic; it springs from the same raw, formless source, but it's channeled through a radically different worldview. It's also genuinely new: whereas magic came and went along the way to the Sixth World, this is the first time metahumanity has seen anything like the Resonance.
The Foundation, then, is rawer stuff than the manufactured Matrix 2.0, closer to the unshaped wellspring of the Resonance's power, and more affected by the fever dreams of the Matrix; hence why it's so trippy. And the Matrix 2.0 itself is powered by the Foundation. Danielle de la Mer's experiment with the technomancers tore a permanent hole through the barriers between the normal Matrix and the Foundation, and let power leak through; that power now makes the Matrix work, and the technomancers being dead doesn't matter because the hole is now is now self-sustaining. Or maybe expanding...!
Hmm, as I'm writing this now I'm wondering what the lived experience of an AI going into the Foundation would be... interesting idea. And now I'm also wondering: if the Horrors come from beyond the Metaplanes, then what will the Resonance version of the Horrors going to look like? Elder Gods from beyond the Matrix! A rampaging Cthulhu with tentacles made of pure data, smashing through the grids!
(I'm not a huge fan of the Matrix 2.0 fluff, but this is the headcanon that I've adopted to make my peace with it.)