Thanks for your help guys. I have a feeling that it is probably a good idea when flat towing to run any vehicle every 200 miles just in case everything isn't getting lubed properly. After a lot of reading owners manuals at dealerships, etc. I've found that a surprisingly large proportion of manual transmission vehicles aren't supposed to be flat towed (I guess for fear of bad lubrication).. Interestingly, Ford approves flat towing of the manual Focus while Mazda does not approve the Mazda 3 and both are essentially the same drivetrain.
Regarding rear locking hubs, I see that that won't work because the rear axle is not full floating so the wheel is bolted directly to the end of the axle shaft.