Centaurus, your logic has merit. The use of autothrottle also has advantages of reduced workload and reducing any tendency to float. This is particularly so with those auto throttle systems which will retard during manual a flare e.g. Avro RJ. (But it’s not always advantageous to use auto throttle during manual flight).
However, as you realise the overrun problem is not just speed at the threshold. When approaching in gusty conditions, the nature of the gust might result in the aircraft either being high or low at the threshold due to the effect of the gust / lull, this and the same wind variability could also affect the longitudinal position of touchdown.
The risk of an over-run might be reduced if crews thought about the risks in the landing (every landing) when planning the approach. There are many factors affecting the risks, and the more that are known / understood, then with appropriate consideration the overall risk should be minimised.
Where consideration to use auto-throttle is part of the pre-landing briefing, then the crew might also be cued to consider other factors (a trigger for thinking). These too should further minimise the risk of an over-run.
General Refs / Info
1.
Managing Threats and Errors During Approach and Landing.
2.
AC 91-71 Runway Overrun Prevention.
3.
Landing Performance of Large Transport Aeroplane.
4.
Running out of runway.
5.
Safety aspects of tailwind operations.