Reactor physics analyses of nuclear cores with nuclear fuel concepts containing tristructural isotropic (TRISO) particles, such as pebbles or compact fuel elements, rely on various degrees of simplification to keep these highly heterogeneous problems computationally tractable. One such limitation regards the level of spatial discretization employed during burnup calculations, where traditionally only a limited number of spatial zones are modeled at the full core level and assume that the spectrum is constant within the fuel elements and TRISO particles in this depletion zone. This type of assumption neglects the impact of spatial self-shielding effect within the kernels (microscale level) as well as within the compact or pebbles (mesoscale level). The Monte Carlo code Serpent 2 contains many relevant features for efficiently modeling this type of geometry, including a collision-based domain decomposition intended for very large burnup calculations, which we leveraged for this work to quantify the impact of capturing neutron flux variations occurring at the micro- and mesoscale level on a series of high-temperature gas-cooled reactor fuel element depletion problems. While spatial self-shielding is observed at both scales, with differences from a volume-averaged burnup of ±7% within the kernels and ±2% between TRISO particles within the fuel element, the conjugated effect on nuclide inventories and multiplication factor are negligible, hence confirming that assuming a single average spectrum value may be sufficient for most applications.