I'm not sure how or why the Employer (client) has used Option A with a BoQ, presumably you have some Z clauses to sort out the mess?! Option A uses an activity schedule not a BoQ and the risk of changed quantities would normally be the Contractor's. Option B however does use a BoQ and the risk of changed quantities would then be with the Employer.
The first point to understand is the contractual status of the tender drawing, is it part of the Works Information? If so then you should have entitlement to a compensation event, unless Z clauses have been used or other contract terms introduced for example through incorporation of the tender documents and / or tender queries & responses. If the tender drawing is not part of the Works Information then you'd need to look more closely to understand whether you have accepted the risk of changed quantities in some other way.
Option A uses an activity schedule, not a BoQ, so what does this activity schedule look like, check what is referred to in your CDpt2? If the BoQ is not the activity schedule, and not otherwise incorporated into your contract, again you may have accepted the risk of changed quantities (subject to the comment above about the status of the tender drawings).
You were right to notify this as an early warning, as this matter could affect T/C/Q, regardless as to who ends up paying for the extra 100m2.
Unfortunately the Employer is not using the contract as intended by NEC, based on the information you've provided it's impossible to shed much more light on this without seeing the contract documents.