It depends on what Main Option you are using.
If option A (priced contract with activity schedule) or option B (priced contract with bill of quantities), then payment is made against implemented CE's only, as they are then added to the activity schedule or bill of quantities, respectively, which is the document used to assess interim payments.
For option C (target cost with activity schedule), option D (target cost with bill of quantities) or option E (cost reimbursable) then the payment mechanism is based on 'actual' cost, so would include any costs expended against CE's whether they are implemented or not, as the CE assessment is used to adjust the target or budget (Prices).
If option A (priced contract with activity schedule) or option B (priced contract with bill of quantities), then payment is made against implemented CE's only, as they are then added to the activity schedule or bill of quantities, respectively, which is the document used to assess interim payments.
For option C (target cost with activity schedule), option D (target cost with bill of quantities) or option E (cost reimbursable) then the payment mechanism is based on 'actual' cost, so would include any costs expended against CE's whether they are implemented or not, as the CE assessment is used to adjust the target or budget (Prices).