There are assumptions made about x and y that don't apply in your case. If you don't reshape x here <https://github.com/pyqtgraph/pyqtgraph/blob/0a936a4dc0729f67971dcae3cda4c52ad9b0c8a5/pyqtgraph/opengl/items/GLSurfacePlotItem.py#L106> and y further down in the code, then you get what you expect I believe. Supporting two-dimensional x and y would seem like a useful addition and a relatively simple one at that.
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