No, the Null's cross trained standard clone to be Spec Ops, the Alpha series retrained the Commanders. Agreed, Ventress did cut Alpha 17, actually causing paralisis which in teh SWU is a cureable condition, however, he did not die. In fact he wanted to continue to fight. He was put on a medical vessel for transport to a facility to fix him along with what was thought to be Ventress' corpse. However, she wasn't dead she was in a Sith meditation. She ended up hijacking the vessel. Then, apparently in some story that has yet to be written, Alpha 17 makes it back for the second battle of Kamino.
I haven't read the Star Wars chronicles you're refering to. Everything I rattling off is coming from Starwars.com and Star Wars Insider magazine.
I do agree that the Clone Wars Ccontinuity is getting more than a bit convaluted though. Too many cross staories, cross characters etc. To be honest, I'm not really sure how "cannon" I consider the new animated series though. It seems more to be entertainment for children as most of what it does contradicts or clouds the current known continuity. Or, perhaps Luca will say "all the rest is rubbish, the cartoon is how it went down." Who know's.
Anyway, sorry for the off topic rant!
Back to the topic of Phase II ARC's. I would think the basic Phase II ARC kit is essentially what the 327th Star Corp (Bly's guys) wear. However, the ARC's being as independant as they are, probably assembled kits however they darn well desired and mission specific at times as well.