UPDATE
So far so good. No more messages and the car seems to be behaving differently in that iStop function seems to activate much sooner after a cold start than previously, which suggests that the battery is being recharged much more quickly.
However, I still have the warm start (judder and stall) issue though, and have asked the dealer to contact MAZDA UK to see if they are aware of the problem (which does not throw up any DTC fault codes).