Not sure at what percentage of his HP it is, but probably roughly around 10-5% **** get up on his 2 legs and from there on out, he seems to really hit hard. I remember him DA countering me and that 2nd counter going through and hitting me for 600 damage along with a crit for 500 or more. At that mark, hes like a little rage omega imo, seems to spam hate reset move and counter more. I generally stop tping at that stage as atonement wont do anything anyhow when hes on 2 legs. Its not really hard, but most ppl like to just sit there and farm his pods, so ya.
He goes into his final phase at 25%, as Naix said. This isn't his normal 2-leg phase. You're correct that prior to 25%, 2 legs means he's 90+% resistant to magic damage, so Atonement won't do anything. After 25% however, he's only 50% resistant to both magical and physical, so Atonement will cap around 375 with full hate. Can't say I've ever noticed a significantly increased counter rate in this phase, but its a hard thing to eyeball.
Also at 25% it would seem like he spams hate reset, but that's just because at that point he only has 3 TP moves: Colossal Blow (hate reset), Laser Shower (frontal AoE), and Pod Ejection. This is opposed to the 4 or 5 moves he has in normal 2-leg form, along with the fact that he doesn't use hate reset in 4-leg form.