I really don't understand people's obsession with that particular retcon.
Yeah, but if you... man, we're getting into weird analogy territory, like if you disintegrated Superman's arms he wouldn't be able to go "fool! Little did you know that my arms and I are one and can be remade from me!" and will his arms back into being from pure nothingness. - Pendaran
Arx Inosaan
Was Molecule Man always that powerful, or was that whole "Peer of the Beyonder" thing an explicit power up, or even another retcon altogether?
Molecule Man was comparatively normal but then his experiences during Secret War and his enlightenment as to the scale of his powers by Beyonder Doom left him exploring his own abilities. This resulted in him realising that he was insanely more powerful than he thought and in fact a peer of Beyonder and such other ridiculous things.
So... not an explicit powerup, since he always had that level of power to begin with technically, but his powers definitely increased in scale after Secret Wars.
To be more precise, when he got his powers, he had two huge mental blocks - normal, because he was a pretty weak-willed guy. Problem 1: Could only affect non-living stuff, and Problem 2: he needed his wand to do anything at all. His early losses came when people took the wand away, leaving him a helpless chubby dude. That block went away sometime around Avengers 250-ish. There was a scene where Cap busted through to grab the wand, and snapped it, only to have Reece still function just fine. Some exposition explained that he'd realized it wasn't the wand.
The second block to go was the "living stuff" block. Doom released that during SW, and also showed that he was just generally more powerful than he thought. He still wasn't exactly a peer of the Beyonder (or Beyonder-Doom), but he was good enough to be able to bring all of the bad guys back from SW, etc. The "peer of the Beyonder and second-strongest dude evah" stuff came in SW2, when the assembled cosmics, including the LT, came to him begging for him to save their butts.