East Fishkill will be ready first, so production will start there first. The earlier sampling and higher-scale production can start, the more testing is done, and the more mature the process will be. The better-off the testing, the better and earlier the processes can be replicated in Nagasaki and Oita and follow similar lines--or improved ones depending on what is discovered in Fishkill's production. The earlier and better production is, the earlier and better they can test the chips externally. The sooner any refinement can be made to the lines if necessary. The longer they have to test the PS3 as a whole unit and make adjustments to anything ELSE. The more kits can be created. The more chips can be ready for a broader launch. The more CELL chips are available for separate uses and testing.
With Fishkill already set for CELL production, why spend the time and money to shift it? It would still have the most mature processes, and likely be the easiest to experiment with working with IBM engineers. (Not to mention why would Sony invest so much in Fishkill if it was expected to shift lines the moment Nagasaki and Oita #2 were up and running?) And extra production is always useful. If not all the lines of Nagasaki #2 and Oita #2 are needed specifically for PS3 chip production, then they'll be moved to other SoC solutions for other devices as well. (If as stated production for PS3 is aimed for 15,000 wafers/month, then they'd also be aiming to have headroom should problems arise. If capacity is improved over time--as the Oita article states, moving to 12,500 wafers/month itself by FY2007--then they may be hoping demand keeps going and they can provide it, or they're encorporating other lines or the same chips for other devices as well.)
Eventually any of the fabs could be retargetted--and perhaps Sony's agreement with IBM in East Fishkill has a maximum duration--but why is any of what we've seen thus far questionable? We've known how big an endeavor it is for them for a long while.