I don't think it's a bug.
As far as I can tell, that's because the 3D program where you created your multilayered file does layer blending in linear space and GIMP with GEGL off does it in gamma-corrected space.
When "use GEGL" is selected, GIMP does the layer blending in linear space too, then you get similar results in both applications.
Some blending modes like overlay look very different in linear and non-linear space.
I'm not 100% sure, but it looks exactly like that.
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