Practicing on clay seems to me to make South America more likely than indoor Europe, although of course both are still quite far away in the calendar.
Far away yet not too far either if he aims for Sao Paolo - 6 weeks. Could do Sao Paolo, week off, Acapulco, IW, Miami. Or maybe skip one of IW and Miami if needs be. Could get match practice on clay and general confidence against lower ranked opposition prior to Monte Carlo. Better than getting that practice at a slam or Masters. It would not be beyond him to win those clay tournaments too - 750 points before IW would not be bad given he hasn't earned any points since Wimbledon.
Personally I think they're being cautious as they don't want to in any way jeapordise the clay/grass season - his best chance at titles and points. Try and peak then - if he wins RG then the season is a success no matter what else happens. Some of the pessimism about his future seems misguided to me - just think his priorities are different - will go for the titles he thinks he can win and pare down schedule rather than fighting for everything and potentially worsening knee problems.
RG and Wimbledon will always be easier for him than US Open and Australia - particularly with Novak and Murray around. Could be a very wise decision indeed to skip Australia and let the others battle it out in the heat.