This is due to limitations of Wine that won't be fixed.
While Windows processes running under Wine can start native processes, they cannot wait for a native process or interact with it via pipes once it is started.
There are plenty of ways around this, but they all involve some work on your part. You could, for example:
- Use a Windows build of the programs you need to use (probably not an option, I take it).
- Use a .sh script that executes the program you want and redirects the input/output using files.
- Write a winelib program that acts as a proxy for the native Linux process, funneling information between the Wine and Linux pipes.
- Use a Windows ssh client to run Linux programs on localhost.