Hi Suzanne- I love these use cases, and I have an example like this right in front of me.
I think what you may have happening here is simply a rendering issue with immediate subsurface 2D symbols. Even though you've removed the basemap in your scene view, the 2D point symbols are conflicting with the elevation surface and irregularly rendering. You can check this by navigating under the surface-
- In the Contents pane, choose the Ground elevation surface.
- On the Appearance tab, check the Navigate Underground checkbox.
Even though it is possible to vertically exaggerate these readings, I would advise against it before producing an analysis product with 3DEBK as it's expect real-world inputs and the results will differ with exaggeration. You're also able to set a vertical exaggeration for Voxels.
I'll tell you how to do it anyway
Exaggeration in Pro is a per-layer setting. Under Layer Properties->Elevation, you'll find a vertical exaggeration parameter.
If you intend to publish or share this layer outside of this Pro Project,you'll need to us the GP tool "Layer 3D to Feature Class" to "burn" the geometry exaggeration changes into the feature.
So- cool about the workflow afterwards. Definitely check out the 3D Empirical Bayesian Kriging tool, which can take numeric values and interpolate data. There's a recent tool with Pro 2.6 where you're able to export 3DEBK results to netCDF to be read as Voxels in Pro 2.6 Advanced.
I have a similar example here with soil density borehole values under a large piece of infrastructure:
Really interested in your results!
Phil