There are several cases where county court judges have found on favour of passengers who were effected by knock on effects of "extraordinary circumstances". The test IMO seems to be that the delay clock begins at the moment a replacement aircraft could theoretically be provided to to fly from A to B, irrespective of the practicalities.

Bad weather must also affect the ‘flight in question’ in order for airlines to use it as a defens according to Bott + Co.

A very politically correct CAA statement
"A delay caused directly by bad weather is generally considered outside an airline’s control and therefore airlines do not have to pay compensation," he said. "However, if an earlier delay is affecting later flights – or causing a knock-on effect - airlines may find it harder to demonstrate that they have taken all reasonable measures to avoid disruption. If they are unable to do this, passengers may be entitled to compensation as the airline has been unable to prove the delay was unavoidable."