Unfortunately is not possible on Windows 2012 R2 Remote Desktop Service App define a StartIn/Working folder. I had a Java Application that require a specified working folder to run without problem.
The workaround is to create a batch and publish this batch instead of application:
Start “%ApplicationName%” /d “%path to startdir%” “%path to executable%”
Then change the icon of published application following this guide: https://241931348f64b1d1.wordpress.com/2016/09/07/how-to-change-remote-app-icon-on-windows-2012-r2/