So why didn't all the superpowered Earth-2 Kryptonians survive the explosion of Krypton? Is invulnerability hit by the extreme G?
My understanding is both Kryptons had red suns so they both had invulnerability derived from our yellow sun. Siegel established early on in Action Comics #14 that the GA Krypton's sun was red. Also, whatever anti-grav capability they evolved to help counteract Krypton's pull was likely 'unloosed' when free of that gravity to provide an anti-grav aura of protection like Lana Lang's 'gravity' belt did for her.
"Negative Crisis on Earths One-Two" was indeed the JLA/JSA story where the two Supermen fought to a standstill. When they faced Krogg in the 1970s, they still were considered equal. Even when Kal-L was later in the 1980s depicted as somewhat weaker than Kal-El, he still was in the same range (the difference between two men not a man and a gnat). Kal-L was still capable of super-speed time-travel and notably knocked out Kal-El and dealt the final blow to the Anti-Monitor during the Crisis.
E-2 Superman is arguably much more powerful than the Byrned Superman since he's almost as powerful if not as powerful as the E-1 model.