There is nothing to stop you breaking a compensation event down into smaller elements so that it allows for individual elements to be paid as they are completed. There is nothing to say that a compensation event has to be a single line. I am aware of a recent CE on one project at over £1million and be carried out over six months - that would not be fair if it was only a single line item on activity schedule.
For completeness. you could submit a revised activity schedule for acceptance under clause 54.1 with this broken down into detail. The Project Manager has no reason not to accept as long as the activity schedule is in line with the programme, adds up to the correct total of prices and costs are “evenly distributed”.