The bikes look rather different. The front shocks are different. Likely the Hi Fi 29er is going to be significantly more expensive, so they will serve different markets. Maybe this is why Fisher is using Fox for the front fork, rather than having Manitou slap together a longer fork.
IMHO people will pay a significant amount more for the fox fork. So if both platforms work out, they will both be here for a while. If one has a serious problem (like the Hi Fi 26er "folding" issue, or the Sugar frame cracking) Fisher will be glad to have a back-up FSB platform.