You post reeks of frustration !
So, firstly, If it is a major Defect which prevents the Employer from using a the works, then the Contractor will jot have achieved Completion.
Secondly, under both options A & B, for payment purposes completed works means which is does not delay or be covered up by immediately following work. In other words, some of the Defects may affect their cash flow.
Secondly (again), if under option C to E, some Disallowed Costs are associated with doing work which results in Defects, including correcting any Defect after Completion.
Lastly, you do not have to do a deal to get a Defect corrected as per clause 44 of NEC3 ECC / clause 45 of NEC4 ECC. Instead, if they do not correct i by Completion then (a) it would be more expensive for the Contractor to correct and (b) if they do not, then you can charge them the cost of getting others to correct it, which will be even more expensive.
You may wish to notify an early warning on the basis that poor workmanship may well "impair the performance of the works in use", point out the above and discuss a sensible way forward which balances quality with time (the Employer's objectives) and profit for them.