Keeping in mind that the FastXOR output is generally easier to use to identify differences, you could use the "-include_layer <file>" argument. The file should have each layer you want to include on a separate line, using the same syntax you would for a LAYER MAP statement.
The information on DBdiff has moved around a few times, and you don't say which Calibre version you are using. Try searching the bookcase for "DBdiff" -- it will likely be in calbr_ver_user, calbr_solns_pv_user, or (2017) calbr_lvl_fdi_gd.