In Option B the employer takes the risk, or reward, of the quantities in bill of quantities being higher or lower. Clause 11.2(28) makes it clear that the quantities in the bill of quantities are remeasured. However, remeasurement is not the case if the change of quantities was caused by a compensation event. In that case, the compensation event is assessed based upon the effect it has, or is forecast to have, on the defined cost plus the fee, see clause 63.1. Once assessed, the bill of quantities is changed in accordance with the rules in clause 63.13.
As for clauses 60.4 and 60.5, these rely upon the change to the total quantity of work done as compared with the quantity for an item in the bill of quantities. Therefore, it is not a compensation event if it is the cumulative effect of changes made to several items in the bill of quantities. However, it is not clear why your bill of quantities is not aligning with the works information.
If it is because of the quantities, the first paragraph of this answer deals with it. But if it is an error, ambiguity or inconsistency, clause 60.6 requires your project manager to correct the listed errors in the bill of quantities. Each such correction will be a compensation event and will be dealt with in accordance with clauses 63.1 and 63.13. Note when assessing this compensation event, the contractor is assumed to have taken the bill of quantities as correct, see clause 60.7.
As for dealing with time, the contract is consistent in that a compensation event can never result in the completion date being set to an earlier date. That is because of the wording of clause 63.3, which refers only to delays to the planned completion.
All of this is confirmed in the NEC3 Engineering and Construction Contract Guidance Notes on clauses 60.4 to 60.6 and clause 63.3.