This is a bit of a wishlist without much grounding in how these tools actually work.
Emacs doesn't "depend" on gnuplot in any meaningful sense. org-babel can use it, but it's optional. The request for "custom and actual GNU bound 3d plotting software" is vague to the point of being meaningless. What would that even be? Gnuplot is already GNU-adjacent and works fine.
calc.el is already bundled with Emacs and has been for decades. It doesn't need gnuplot at all for its core functionality. You want 3D plotting integrated with calc or something? You can just build one - elisp is not that hard, LLMs these days understand it better than some other, traditional PLs.
Plotutils - is an obscure GNU package that's largely unmaintained. Advocating for it as a "mandatory" dependency in 2026 is puzzling. The project is essentially dead upstream.
Last thing is Texinfo project problem, not really an Emacs one.
You seem to have a bunch of opinions about GNU software purity rather than someone who has hit concrete practical blocks. Emacs is for pragmatists - you either solve a problem on the spot (without complaining about the purity of the solution); ask if someone done that already and use an existing package; or just put a TODO note in a .org file and deal with that later.