Yes this probably does go against the spirit of the contract and clause 10.1 - but I am afraid this will not help you contractually or I believe in adjudication. there is no time limit within the contract when disallowed costs can be assessed.
The flip argument is that if something is dis-allowable then it shouldn’t have been paid. The fact you are being told this only at the end when you have little/no time to do anything about it is unfair in a practical sense. Many clients claim they will not do this and put in place regular audits to avoid such issues and ill feeling.
NEC4 has recognised this issue by putting in place a mechanism for the Contractor to ring fence elements of defined cost and put that in for “final” assessment mid-project. The Project Manager/Employer is obliged to assess within a certain timescale, and there is even a point they can become deemed accepted if they are not responded to. But, this is NEC4 not NEC3.
I can only symphasise in this case(which will be little consolation) - and suggest your efforts as a Contractor are focused on contractually whether individual items are right to be disallowed, rather than whether the principle of doing disallowed costs generally at the end is fair or not.