A lot of applications use commercial components, that tend to be tethered to windows security models for registration/activation reasons.

Many internal apps likely don't need to target windows, but may have windows-isms baked in for a number of historical reasons. There are also a lot of .Net apps tethered to windows more out of heritage, most are easy enough to port, others much harder, it varies and there's a lot of apps unlikely to receive the effort to even explore the feasibility of migration to either mono or dotnet-core.