I'm not sure I understand your concern. The N6 not having LED notifications doesn't impact how lightflow works on N5.
Anyway, if you are not getting repeated LED notifications for Messenger on the N5, try to backup your settings, and then wipe data/cache for the Lightflow App and try to set up your preferences once again (don't restore settings). I use Lightflow with Messenger on my N5 and it works as expected. Maybe something got corrupted with the settings?
You can also just try to contact the developer from the play store link - he is very responsive and actively works with the users to help troubleshoot and resolve the issue. He may have better suggestions than the one I suggested above.