It's possible it may just be that ffmpeg requires specific ordering for some flags, but I was asked how to have segment filenames prefixed with a FQDN within the generated manifest.
The answer should
./HLS-Stream-Creator.sh -i example.avi -s 10
Which should lead to the segment filenames within the manifest being prefixed with the FQDN.
For some reason it didn't work, though manually adding that option to ffmpeg within the script worked fine.