--generate-load-scripts for .NET Core appears to create incorrect #r directives

Description

--generate-load-scripts for .NET Core appears to create incorrect #r directives as it's including GAC references.

Repro steps

paket.dependencies

source https://nuget.org/api/v2
nuget Newtonsoft.Json

Run:

.paket\paket.exe install --generate-load-scripts load-script-framework netstandard1.6

Expected behavior

The produced CSX file contains only references to physical DLLs from packages folder.

Actual behavior

The produced CSX file contains GAC references too.

#r "System.Xml.Linq" 
#r "System.Xml" 
#r "mscorlib" 
#r "System.Core" 
#r "System" 
#r "System.Runtime.Serialization" 
#r "System.ComponentModel.Composition" 
#r "Microsoft.CSharp" 
#r "../../../packages/Microsoft.CSharp/lib/netstandard1.3/Microsoft.CSharp.dll" 
#r "../../../packages/Newtonsoft.Json/lib/netstandard1.0/Newtonsoft.Json.dll" 
#r "../../../packages/System.Dynamic.Runtime/lib/netstandard1.3/System.Dynamic.Runtime.dll" 
#r "../../../packages/System.IO.FileSystem.Primitives/lib/netstandard1.3/System.IO.FileSystem.Primitives.dll" 
#r "../../../packages/System.Linq/lib/netstandard1.6/System.Linq.dll" 
#r "../../../packages/System.Linq.Expressions/lib/netstandard1.6/System.Linq.Expressions.dll" 
#r "../../../packages/System.ObjectModel/lib/netstandard1.3/System.ObjectModel.dll" 
#r "../../../packages/System.Reflection.Emit/lib/netstandard1.3/System.Reflection.Emit.dll" 
#r "../../../packages/System.Reflection.Emit.ILGeneration/lib/netstandard1.3/System.Reflection.Emit.ILGeneration.dll" 
#r "../../../packages/System.Reflection.Emit.Lightweight/lib/netstandard1.3/System.Reflection.Emit.Lightweight.dll" 
#r "../../../packages/System.Reflection.TypeExtensions/lib/netstandard1.5/System.Reflection.TypeExtensions.dll" 
#r "../../../packages/System.Runtime.Handles/ref/netstandard1.3/System.Runtime.Handles.dll" 
#r "../../../packages/System.Runtime.Serialization.Primitives/lib/netstandard1.3/System.Runtime.Serialization.Primitives.dll" 
#r "../../../packages/System.Text.RegularExpressions/lib/netstandard1.6/System.Text.RegularExpressions.dll" 
#r "../../../packages/System.Threading/lib/netstandard1.3/System.Threading.dll" 
#r "../../../packages/System.Threading.Tasks.Extensions/lib/netstandard1.0/System.Threading.Tasks.Extensions.dll" 
#r "../../../packages/System.Xml.ReaderWriter/lib/netstandard1.3/System.Xml.ReaderWriter.dll" 
#r "../../../packages/System.Xml.XDocument/lib/netstandard1.3/System.Xml.XDocument.dll" 
#r "../../../packages/System.IO.FileSystem/ref/netstandard1.3/System.IO.FileSystem.dll" 

Known workarounds

When processing the file, it's possible to manually strip away the offending references.

Reproduce the issue with the shown paket.dependencies file and the --generate-load-scripts load-script-framework netstandard1.6 command. Trace the implementation of load-script generation and compare the produced CSX references with the expected physical DLL references; done means GAC references are absent.