Do the Appendix A, Standard Exclusions override the scope of work in the Specifications?

Yes. In many project documents there are references to the specification not being considered as the method by which the work is divided among the Subcontractors (Example CCDC, General Condition, 1.1.8). Hence, most Bidding Authorities do not expect that they need to amend specifications to align with industry standards for trade scopes of work.