I'm not sure that red skies and all indicate fifth dimensional attack, simply supra-universal attack. It represents the bleed being breached, spilling out. The 5th Dimension had nothing to do with the original Crisis, but that is obviously where Morrison is getting his inspiration for all the Red skies stuff, why he used it in Final Crisis in the same way, etc.
A proto Super-Doom could as likely be the villain who killed Superman on "Doomsday" as any, but so too could the original Doomsday. It's left undefined, but I'd bet dollars to donuts that a later writer will come in and establish that it was just the standard Doomsday.