Since the generated files are similar to binary files, they should not be part of your project or be added to the source code.
In previous versions of TypeScript, the presence of files in the project / under source control could cause problems on the assembly servers in cases where the assembly server did not pay attention to changing files under source control.
Another issue with the presence of files in the project / under source control is that even if you do not modify your TypeScript file, the generated files are re-created during assembly and collected by version control clients as if they were changes. All of them will be displayed as revisions if you checked them (or you have to manually exclude changes to avoid contamination of your original storage).
A new call to the generated files makes them more similar to your .NET DLLs - they are generated on the build server (and locally on your disk), but you do not need them in the source control.