If they are in fact replacing everything but the cases, I don't see why they couldn't use the new style cam plate/cams/tensioner's/roller chain/oil pump. I seriously doubt the parts cost would be much different, and the labor cost is the same. While still not totally proven versus a gear drive setup, I fully believe the new chain system will be much more reliable than the POS original system.
It's a damn shame the MoCo is getting away with not addressing this ticking time bomb in the earlier Twin Cams. IMHO, a reputable organization would at the very least extend the warranty like they did on the '99 cam bearings. And the fact that they still do not publicly acknowledge this issue, and still do not have an official maintenance/inspection interval, is totally ludicrous.
One of the things I have on my list of things to do this fall; replace the tensioner's and check the oil pump. The bike will have less than 20k miles at that time, and based on recent changes in the behavior of the oil pressure gauge I'm expecting to find chunks missing from the tensioner's at the very least (acts like the bypass valve is sticking a little, or could just be a sticky sending unit). One thing I do know, if mine blows Harley will be given an opportunity to make it right (out of warranty, but as far as I'm concerned it's still their responsibility). If they decide to blow me off, I'll fix it myself with aftermarket parts. Maybe I'm just a hardheaded old fool, but I'd rather scrap the bike before I'd let them make any additional profit while I fix their screwup.
Jerry