ts-loader: Can't import plain d.ts files when transpileOnly=true

This is actually the exact same issue as I have with awesome-typescript-loader: https://github.com/s-panferov/awesome-typescript-loader/issues/225:

I have a shared module for shared interfaces between my server and my client. It contains several d.ts files with interfaces I share between my server and the UI. When I use ts-loader everything works as expected, when I use this ts-loader with transpileOnly=true I get:

ERROR in ./src/component.ts
Module not found: Error: Cannot resolve module 'shared/data' in ...src/component
 @ ./src/component.ts 12:26-73

The shared/data should be shared/data.d.ts but it doen’t find it. If I add the d.ts explicitly I get this error:

ERROR in ./~/shared/data.d.ts
Module build failed: Error: Debug Failure. False expression: Output generation failed
    at Object.assert (node_modules\typescript\lib\typescript.js:2099:23)
    at Object.transpileModule (node_modules\typescript\lib\typescript.js:53173:18)
    at Object.loader (node_modules\ts-loader\index.js:421:49)
 @ ./src/component.ts 12:31-83

configuration:

'ts-loader?' + JSON.stringify({
                        transpileOnly: true,
                        configFileName: 'tsconfig.webpack.json'
                    })

config file:

{
    "compilerOptions": {
        "isolatedModules": true,
        "emitDecoratorMetadata": true,
        "experimentalDecorators": true,
        "module": "es6",
        "moduleResolution": "node",
        "noImplicitAny": false,
        "sourceMap": true,
        "target": "es5"
   },
   "files": ["src/component"]
}

Not critical workaround is to just change the files to ts files and transpile them to empty js files.