I have run into this on several occasions, with different versions of Pro and Enterprise. As a test I have written a tiny Python toolbox that creates a point layer with one fixed point, the toolbox runs in ArcMap and Pro.
When I publish the tool as a Geoprocessing Service to ArcGIS server (10.6) from ArcMap (10.6.1) the output layers has schema and geometry type.
But when publishing the exact same tool as a Web Tool to the same ArcGIS server from Pro 2.4 this information is lost.
Even if the information are present in the Share as Web Tool dialog in Pro.
Looks like a bug, or are there some extra steps necessary in Pro?
Problem looks a bit like https://community.esri.com/message/775678-publishing-a-gp-service-with-an-operational-layer, but Geometry type are correct in both ArcMap and Pro so I guess the problem lies somewhere else.
Any ideas Jonathan Quinn?
I am experiencing this issue as well when trying to push a geoprocessing tool via the Service Editor in ArcMap 10.6.1.
I created a python script and embedded it into a tool. The script runs fine and generates solid output features. However, when I try to publish it as a service, the geometry and schema have disappeared in the Service Editor. I have experimented with setting the schema in the tool parameters to match where the input features are stored. No luck so far...
Is there a way the geometry and schema can be restored?