Hello VVuhony,
if the entire extent of the modeling domain is 750 km x 750 km, seeing a significant boundary condition contribution to both concentration and deposition fields as shown in the pie charts in your first post may not be unrealistic. However, I am not familiar with the circulation patterns in this region and local and regional emission sources to have a good conceptual picture of the relative importance of the processes governing pollutant transport, transformation, and deposition at multiple scales.
You are correct that the avprofile_saprc07tc_ae6_aq_derived_from_cb6r3m_ae7_kmtbr_hemi2016_v53beta2_m3dry_col051_row068.csv file distributed with the CMAQ source code represent annual mean conditions in a rather clean remote marine environment derived from an 2016 hemispheric CMAQ simulation. As such, these conditions likely are too low compared to actual conditions for most species for your region of interest.