Hopefully double posting isn't frowned upon here, but I'm not sure how else I can mark this as answered if I figured it out myself (or even if it's alright to mark this as answered if I don't actually have version 3.0). I checked a second time to see if the eye laser behavior was just dummied out. The first time I missed it, but in CNaraku.st, there's a variable, var(56), commented as "Nightmare Mode Enabler." The only place it shows up is in the satellite laser's StateDef, as part of line 1927's trigger. I commented that trigger out and it seems like the eye laser behavior has returned.
reylaesper got a reaction from CoolAnimeHustler in Cyber Naraku by RicePigeon, but version 3.0 instead of 3.1