In simple test, like reading the properties (CRS, geometry...etc) of a shape file we found no issue....even after we removed the 'scratch.gdb' file from (<Installation Directory>\ArcGIS\ArcGISRuntime10.2.4\LocalServer64\ArcToolbox\Templates)
But still we are NOT sure .....is it safe to remove 'scratch.gdb' file.
I'm seeking clarification from the Local Server team. Will reply with an answer shortly.
Okay the word from the Local Server team is that the GDB is needed by some GP tools which need to write content into it. So you could exclude it if you've tested you workflows function correctly.
If however you start using a GP tool which does need it, you may run into trouble.
I think the Geoprocessing Help is quite clear about this. The scratch geodatabase, if used as a geoprocessing environment variable, so called as:
arcpy.env.scratchGDB
is guaranteed to be there. ArcGIS will automatically create it, even if it is not there. See here:
Scratch GDB (Environment setting)—Geoprocessing | Documentation
This makes it safe to write to this environment / workspace even in portable applications / tools.