Can a NEC3 early warning notice also be a project managers instruction?

Agree with all of Jon’s comments - if you can demonstrate that the PM has sought to get a better solution then you should notify a compensation event as per clause 61.3.

You make reference to a 6 month timescale, there is no time bar on Instructions the PM should have given but did not do so. (would be useful to clarify at what stage of the project you are at)

In regard to Disallowed Cost 11.1(25) in an unamended nec3 - corecting Defetcs after Completion is Disallowed Cost and failure to comply with a constraint are Disallowable. You do not state on what grounds the costs are being Disallowed?

If a Defect 11.2(5) is a part of the works not in accordance with the Works Information then work which does not meet the requirements of the Works Information is a Defect but likewise an over specification of work could also be a Defect as this would not meet the requirements of the Works Information.