Is there a way to adjust GM 3D models sitting on ground or place models based on the lowest point elevation of each building/area feature?
For models that have been processed using the Import 3D Objects Utility, the model center locations are assigned to the output database in feature attributes (center_x, center_y, center_z). So, the height of each model assigned in GeoMedia 3D is driven by the value of the center_z attribute, which was in turn derived by Import 3D Objects Utility(FME) from the center location assigned within the input model itself .
While not necessarily recommended, you could update the resulting center_z attribute values where needed (when not originally placed as desired). Also, you could use attribute-based symbology or functional attributes (Expression...) to adjust individual features using the altitude offset value (on the Style Properties 3D Settings tab). Note that the offset value can be positive (to raise in height) or negative (to lower in height).
The root of the issue is in the way the original models were created (i.e. with the center X/Y/Z location of the model being used instead of the Z being assigned at the base of the model).
Another consideration when certain features are not precisely matching the base content surface (for example, when using only the Default_Internet.fly), is to load a better elevation surface for the area of interest (using Add Surfaces, etc.).
If a model feature does not contain the center_x/y/z attributes (i.e. it was placed as a stand-alone model and not from the Import process), the placement in 3D is done using the center point (centroid) of the 2D footprint feature geometry in the database.
Also, there are instances where one or more corners of a model base may be "above" the surface, while the other corners are on or below the surface (usually due to placement on a hillside or other sloping terrain). In these cases, the model will need to be lowered to fully "sink" the base into the surface (or as previously stated, a better surface model may be needed). In either case, the base of a model is not automatically tapered to perfectly align with the contours of the given surface area and may require further adjustments.