NetCDFs support both regular and irregular Z intervals (and probably other problematic things: I don't have full knowledge).
Older versions (pre-3.0?) of Pro refused to display NetCDFs with irregular Z intervals, but recent versions will display them, with an easy-to-miss (for me, at least) warning in the Add Voxel Layer (screenshot from 3.4.3 below - I'd argue that the warning message is misleading, too, as our issue includes the absolute position of the NetCDF).
In our example, the irregular Z interval caused our subsurface voxel layer to be inserted at 0m elevation rather than -5500m; the properties information for the layer indicated that it 'knew' its correct Z location, but the display did not honour this, meaning - obviously - that the layer didn't align with any correctly Z-located data.
When coupled with auto-applied Z exaggerations and other 3D challenges, this sort of thing leads to much head-scratching - or, if you don't notice it, potentially leads to interpretation errors.
One fix, which we had developed previously and which we used in this case when we realized the issue, is to interpolate the appropriate levels to generate a NetCDF with regular Z intervals, using a custom Python tool.
Esri UK support also provided links to (unsupported by technical support) Python scripts that permit this workflow.
Hence it might be appropriate to amend the warning so that it displays a modal dialog when the user attempt to add an irregular voxel layer that provides further guidance as to the issue and potential solutions to it, and perhaps to include tools that support the generation of NetCDFs with regular Z-intervals from those with irregular intervals. Alternatively it would obviously be great if Pro just fully supported NetCDFs with irregular intervals.
The attached zip contains two NetCDFs (containing fake data) that illustrate the issue - one has a regular Z interval, the other an irregular Z interval. In Pro 3.4.3 (at least), the regular Z interval example is displayed at the correct Z origin, the irregular one is displayed at an origin of 0m.