We\'ve gotten a custom action that runs command-line to work as such:
There is a bit of a chicken and egg problem in that an executable has to be marked as a console app before it starts, and if you want to launch such an exe without the console popping up, it has to have its process created with the right flags. If your installer can't provide these, it is possible to use a third .exe in between. For example, the Keybase installer launches this small utility, called keybaserq.exe, in order to run persistent console apps in the background with no flashing black windows. It is open source and you can see how the Keybase installer makes use of it - no flashing console windows.