The OP should put much more weight on MrMustard's opinion than my own given his extensive tribunal experience.
But in my opinion there are two stationary vehicles involved in the circumstances of the stop.
1) The motorcycle - this is directly responsible for the stop but enters the box junction after (or just as) the OP enters the box. On that basis it would be unreasonable to penalise the OP for this as it should not have entered and the OP shouldn't be expected to predict that it would.
2) The red car which turns out of the side road - due to the actions of the motorcycle, we do not have the luxury of knowing how the OP would have traversed the box and therefore whether the OP would have had to stop due to this stationary vehicle. All we can do it establish distance between the OP and the vehicle and the speed of travel to deduce on balance of probabilities if the OP would have "had to stop". As stated earlier, the box length is 10.2 metres (as per googlemaps distance measurer). The time between entry to the box and the red car moving off is 8 seconds (to the nearest second). Travelling across the box at leisurely walking speed (2.5 miles per hour) would mean the red car had moved off by the time the OP reached the other side. That speed doesn't seem inconsistent with the speed upon entry and across the first portion of the box prior to stopping. On that basis the OP did not cause their vehicle to enter such that they (would have) had to stop due to the presence of the red vehicle.
Or am I being too logical?
The letter is dated 11 July but it gives you 14 days from date of service (assumed to be 15 July - 2 business days after posting). Most PCN related deadlines include the day of posting/service as part of the time period so to be safe treat the deadline as 28 July rather than 29 July).