Update released for Logic Apps Enterprise Integration Tools for Visual Studio 2015:
With this update it is now possible to generate and validate Flat File native instances from Flat File schemas.
Do note that for these to work if the Flat File schema was created with BizTalk tools, the extension class in the annotation needs to be updated to match with Logic Apps tools.
<schemaeditorextension:schemainfo xmlns:schemaeditorextension="http://schemas.microsoft.com/BizTalk/2003/SchemaEditorExtensions" standardname="Flat File" extensionclass="Microsoft.BizTalk.FlatFileExtension.FlatFileExtension" namespacealias="b"></schemaeditorextension:schemainfo>
This the value in red should be replaced with Microsoft.Azure.Integration.DesignTools.FlatFileExtension.FlatFileExtension.
Credits go to Preetham Vinod for all of the fix, release and extension annotation note.