None really any legal implications - as long as they do not breach existing law. That is why amendments to the standard form should be vetted and challenged/checked by “experts”. The trouble is that sometimes it is the alleged “experts” that you have gone to for the recommendations in the first place, so they must be right (especially when they have charged you all this money)!! There could be some amendments that could be challenged as “unfair” clauses - but that would be a lottery and I would want to iron those out as a Contractor at tender stage rather than run the lottery of taking that to court in the hope I would win.
Changing the standard words of NEC3 contracts is not wrong - you just have to make sure you understand what you are doing and the reasons that you are doing it for (and that it does not create other issues or ambiguities)
What would be such legal implications if they were to breach existing law due to amendments made to the standard form of contract?
Under the Contract the Contractor can not be asked/instructed do anything illegal or impossible.