I am not sure why that new registry entry is being added, but there are two possibilities of workarounds:
1. Instead of manually adding that registry key, go to the File Association view in the Advanced Settings of a component that contains the EXE to launch as a keyfile. Here create the file extension (this is the MSI supported method for file associations).
2. Instead of adding the key in the ISM and then building, try adding it directly to the MSI.
It is possible that this registry key is being created by MSI to facillitate advertisement of the extension.
-Ajay