We present a comprehensive molecular dynamics study of Doppler laser cooling for 88Sr+ Coulomb crystals (N = 50) confined in a linear Paul trap with controlled structural phase transitions. By varying the end-cap voltage U_ec from 0.5 V to 100 V (Mathieu q = 0.2), we investigate the temperature evolution across the linear, zigzag and ellipsoid structures. Instead of a single global temperature, we employ energy decomposition thermometry to separate the secular (T_sec) and micromotion (T_mm) contributions, and find that micromotion accounts for 60-99% of the total kinetic energy along the whole structural sequence, exceeding 99% in the ellipsoid phase. Binned spatial statistics over five independent runs reveal only weak radial correlations of the secular temperature (fitted slopes between -0.22 and +0.03 mK/µm, R² = 0.17-0.64) with an absolute radial variation below 6 mK, whereas the coherent micromotion scales as r² with a coefficient of determination of 0.993 and reaches more than 1000 mK at the crystal periphery: the crystal thus combines a radially homogenized secular temperature with a strongly position-dependent micromotion amplitude. The axial secular component stays at 1-5 mK, at or a few times above the Doppler limit, at every voltage because it is directly laser cooled, while the transverse components are heated to 4-6 mK in the ellipsoid phase. The crystal is therefore transversely isotropic but remains axially-radially anisotropic. Control simulations in which the RF drive is replaced by its pseudopotential equivalent show that micromotion-induced Coulomb heating supplies about 60% of the secular kinetic energy in the ellipsoid phase, whereas the two configurations agree to within 10% in the linear chain; the micromotion energy is always present, but it is converted into secular motion only in multi-dimensional crystals. A transverse anisotropy of about 30% between T_x and T_y appears in the zigzag regime and weakens in ellipsoids. These findings demonstrate that global averages measure a thermally averaged secular energy dominated by micromotion-induced Coulomb heating rather than local secular temperature variations, with important implications for quantum gate fidelity in scalable ion trap architectures.