Maximum distance separable (MDS) codes and near MDS (NMDS) codes are of particular interest in coding theory due to their optimal error-correcting capabilities and wide applications in communication, cryptography, and storage systems. A family of linear codes is called a family of non-GRS MDS-NMDS codes if for each $[n,k]_q$ code in the family, it is either an $[n,k,n-k+1]_q$ MDS code that is not monomially equivalent to any GRS code or extended GRS code, or an $[n,k,n-k]_q$ NMDS code. This paper develops a unified framework for constructing new families of non-GRS MDS-NMDS codes via deep holes. We show that, starting from a family of $[n,k]_q$ non-GRS MDS-NMDS codes with covering radius $n-k$, one can systematically obtain more $[n+1,k+1]_q$ non-GRS MDS-NMDS codes. The proposed framework is further reformulated in terms of the second kind of extended codes. This reformulation recovers a main result of Wu, Ding, and Chen (IEEE Trans. Inf. Theory, 71(1): 263-272, 2025), provides a provable reduction in the computational complexity compared with the approach of Ma, Kai, and Zhu (Finite Fields Appl., 114, 102844, 2026), and reveals additional structural properties of the resulting codes. As an application, we determine the covering radius and characterize two classes of deep holes of extended subcodes of GRS codes. By applying our framework, we obtain three new families of non-GRS MDS-NMDS codes and investigate the monomial equivalence between the resulting codes and Roth-Lempel codes.