The assessment of weather compensation events is dealt with under clause 63.1, that is by assessing the effect the event had upon the defined cost of the work. However, unlike most other compensation events, this assessment uses the actual defined cost rather than a forecast because the event cannot be notified until after the event has occurred, that is after you can compare the actual rainfall with the statistical average, see the last sentence of clause 63.1. So, you start with the actual effect of the excess rainfall, not a theoretical one.
What the effects are will depend entirely upon the facts of your project. If none of the work was weather sensitive, then the excess rainfall and days will probably have little or no effect upon time or defined cost. Equally if the work was very weather sensitive, for example the contractor was carrying out earthworks and the site became over saturated, it may have an effect for many days more than the actual rainfall duration, with excavation equipment unable to work. So, there is no ‘one size fits all’ answer to your questions, other than ‘it depends’.
A further complication is that the assessment is based only upon the effect the rainfall or days of rain in excess of the once in 10 year average, see the final sentence of clause 60.1(13). Most people tend to take that to mean the compensation event starts when the once in 10 year average is exceeded. So, in your example, the effect of the last 5 days of rainfall is taken into account, but remembering in all this that it is also only the effect of the amount of rain that exceeds 5 mm in those 5 days.
From the above you will see it is important for the contractor to show from its records what the actual effects the rainfall were. It is especially so if you are not regularly based on site. There will need to be some discussions between you and the contractor to come up with a practical method of splitting the costs as to that caused by the rainfall beyond the once in 10 year return average and the rainfall within it.