Yeah, F404 development is interesting, to say the least. Afaik both the notched and un-notched F404s (I’ll classify as “late” and “early” respectively) had the exact same thrust output. The only difference was with the fairing/exhaust petal design. Why was it changed? No idea, found nothing on it. Small sidenote, but I had also noticed a similar design change from the F101 mounted to the 4x B-1As, vs the F101 DFE and eventual F110 seen on the F-16C and F-14B/D.
At least the LERX fences and inner tailfin brackets have a tangible reason (vortices generated by LEX impacts on tailfin, causing major fatigue/possible damage, LEX fences disrupt vortices and brackets strengthen tailfin connection to fuselage, causing way less wear and tear).
Neat to see the centerline holding something more than a singular piece of ord, dunno why gaijin thinks that the centerline pylon cant hold at least MERs to begin with.
