Yes, the bytes are -slightly- inaccurate just like you said. PBP and/or MCS adds a few bytes to the total...or does it?
I'm fairly sure MCS takes into account ALL bytes programmed...config bytes, eeprom, program space, everything.
In my situation, if I add together what the PICKIT software shows as the top of the program, add in all of the eeprom DATA statements, add in the eeprom used by my font, add in the 6 or so CONFIG fuse words, etc, it all adds up to the amount shown at the bottom of the screen by MCS.
Delete all of the DATA and EEPROM statements, and the total comes out to be about 4-6 bytes off. Remove anything resembling a CONFIG fuse from the .inc file, and the numbers are identical.