Basically the "Desert" cfgPatch keeps appearing as a dependency on missions that were created with only "Vanilla" content.
The issue seems to occur when the mission has a "Comment", as seen here:

Steps needed to reproduce the issue:
Start the Editor with a "New Scenario".
Save it with any name.
Check the "Required Addons" to make sure that the "Desert" CUP Terrain addon is not listed as a required addon.
Place a comment, like in the picture bellow.

Save the scenario.
Check the "Required Addons". Now the "Desert" CUP Terrain addon is listed as a required addon.

Reproduced with ONLY CUP Terrain mods loaded: