Do you have any sort of antivirus running on your system? Windows Defender should allow WadSmoosh to run but other AV software might not, and they don't have a process by which I can get it cleared for safe use.
Changing the IWAD filename would invalidate savegames, break config.ini paths, and a few other undesirable things. But if you want to manually rename your generated files and manage that on your own, feel free.