Terrace-sized, single-orientation graphene can be grown on top of a carbon buffer layer on silicon carbide by thermal decomposition. Despite its homogeneous appearance, a surprisingly large variation in electron transport properties is observed. Here, we employ aberration-corrected low-energy electron microscopy to study a possible cause of this variability. We characterize the morphology of stacking domains between the graphene and the buffer layer of three different high-quality samples to capture the range of possible behavior. Similar to the case of twisted bilayer graphene, the lattice mismatch between the graphene layer and the buffer layer at the growth temperature causes a moiré pattern with domain boundaries between AB and BA stackings. We analyze this moiré pattern to characterize the relative strain and to count the number of edge dislocations. Furthermore, we show that epitaxial graphene on silicon carbide in general is close to a phase transition, causing intrinsic disorder in the form of the coexistence of anisotropic stripe domains and isotropic trigonal domains. Using adaptive geometric phase analysis, we determine the precise relative strain variation caused by these domains in different samples. We observe that the step edges of the SiC substrate influence the orientation of the domains and we discuss which aspects of the growth process influence these effects by comparing samples from different sources.