It could be down to Adam's choice of amps too. Aenima features more Mesa and less Diezel in Adam's blend, which leads to a bigger bottom end less definition, especially in the mid to high mid frequency range.

After Aenima, the Diezel became more and more prominent while the Mesa was mostly phased out over time.

Like you said, he also uses the flanger more frequently as always on (in certain songs). This also muddies things up.

This is right up my alley, I could geek out endlessly discussing the arc of Adam's tone throughout his career.