The roll center is indeed lower on series 2 knuckles (we tested it this year in a very round about way)

The S1 ball joint hole in the knuckle is smaller than the S2's hole in the knuckle. 27mm vs 30mm IIRC?

 

the S1 vs. S2 lower front ball joint stud taper difference is documented, but first time I’ve heard of there being a front roll center difference. The S2 lower ball joint has the same taper as the NC Miata. The NC Miata upright is approx. 1lb. lighter than the RX8, but likely easier to bend in wheel-wheel racing contact. Might be an option for autox where allowed.

It was the S2 rear suspension that Mazda claimed had a geometry difference, but all the rear control arms are the same length as the S1. That would lead me to believe there was either a rear upright difference and/or rear subframe difference, and/or chassis/rear shock-tower difference.
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So I've been trying to figure out what alignment settings to aim for on my Rx8. Car is NOT a daily, and will get used on various tracks with the occasional AutoX. I've come up with these alignment settings so far and looking for some input.

Front:
Camber -2.5
Caster +6.0
Toe -0.1

Rear:
Camber -2.0
Toe +0.1

I would actually like to try and get -3 front camber and -2.5 rear camber, not sure if ill be able to reach those numbers however.

Car has KW V3 coilovers, I'll have to remeasure the ride height from hub center to wheel arch as I don't recall offhand what it is set to. Sway bars progress tech front and oem r3 orange dot rear, links are evo-r adjustable links f/r tying everything in the suspension up.

 

That's a great start. -3f/-2.5r will feel great at both track and autox, and -4f+ will feel even better for autox. I haven't done any high speed tracks at -4f yet, but it felt good at a smallish track up here in NH where I hit 90 something mph. Mazda motorsports sells a lower knuckle bushing for the front that will give you more camber, I got nearly a full degree out of it.

 

it will depend on the tires, but also relative to tire width vs wheel width.

and suspension choices too.
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I dont have a dedicated tire right now as far as TW is concerned, but tire size is 245/40 on a 18x9.5+35 (all squared). Ive contemplated bumping up to 265/35 squared if the benefit would be positive overall, given forced induction adding more power to the rear end