We quantitatively evaluated lattice plane microstructure, which includes lattice plane tilt, spacing, twist, and their fluctuations, in a modified Na-flux GaN bulk single crystal using the synchrotron-based nanobeam X-ray diffraction method. The GaN crystal was fabricated by two-step growth; the first layer had coalescence boundaries as a consequence of faceted growth from the multipoint-seed GaN template, and the second layer grew on the first without faceted growth. Position-dependent ω-2θ-φ mapping analysis revealed in-plane distribution of local lattice plane microstructure along with dislocation morphology around the coalescence boundary and the growth-stage boundary (GSB). Faceted growth from the multipoint seed template led to concentration of a-type dislocations at the coalescence boundary. These dislocations would glide widely on basal planes above the GSB, and then homogeneously propagate toward the surface. As a result, the modified Na-flux GaN crystal had a homogeneous lattice plane microstructure with little bunching of threading dislocations.