With the recent discovery of in-plane chemically ordered MAX phases (<i>i</i>-MAX) of the general formula (<i>M</i><sup>1</sup><sub>2/3</sub><i>M</i><sup>2</sup><sub>1/3</sub>)<sub>2</sub>AC comes addition of non-traditional MAX phase elements. In the present study, we use density functional theory calculations to investigate the electronic structure, bonding nature, and mechanical properties of the novel (W<sub>2/3</sub>Sc<sub>1/3</sub>)<sub>2</sub>AlC and (W<sub>2/3</sub>Y<sub>1/3</sub>)<sub>2</sub>AlC <i>i</i>-MAX phases. From analysis of the electronic structure and projected crystal orbital Hamilton populations (pCOHP), we show that the metallic <i>i</i>-MAX phases have significant hybridization between W and C, as well as Sc(Y) and C states, indicative of strong covalent bonding. Substitution of Sc for Y (<i>M</i><sup>2</sup>) leads to reduced bonding strength for W-C and Al-Al interactions while <i>M</i><sup>2</sup>-C and <i>M</i><sup>2</sup>-Al interactions are strengthened. We also compare the Voigt-Reuss-Hill (VRH) bulk, shear, and Young's moduli along the series of <i>M</i><sup>1</sup> = Cr, Mo, and W, and relate these trends to the bonding interactions. Furthermore, we find overall larger moduli for Sc-based <i>i</i>-MAX phases.