Actually, I think all the examples you provided were independent dimensions. I'll concede orthogonality.
More specifically: can you think of coordinate systems with explicit binary or ternary constraints on the parameters in the coordinates? I can't immediately think of any.
Holonomic constraints etc. are constraints on the validity of regions of the space, not constraints on the ability of coordinates to exist.
If I understand correctly, homogeneous coordinates have additional independent dimensions, but are many-to-one instead of constraining their parameters. Maybe normalized homogeneous coordinates? That's not a particularly interesting system.
I'm now second guessing my definition of coordinate system...
Would points in a simplex qualify as a coordinate system? Their dimensions would have to sum to 1. That is, so-called "normalized" barycentric coordinates maybe, as opposed to standard barycentric coordinates?
https://en.wikipedia.org/wiki/Coordinate_system
https://en.wikipedia.org/wiki/Curvilinear_coordinates
https://en.wikipedia.org/wiki/Skew_coordinates
https://en.wikipedia.org/wiki/Generalized_coordinates