I don't see how it could be.
Even using the advanced speciality closest to your speculation, the Space Wolf Scout, we see it even states "Tactical Marines only." So even the wolf scout is a tactical marine, and has a tactical marine special ability although he also gets his scout special ability as well. Yes the characteristic advance table changes, but you can't purchase these advances until you can purchase the scout specialty anyways. None of the advanced specialities, so far, have their own advance scheme for all 8 ranks, you still have your primary speciality no matter what advanced one you chose.
You can only choose an advanced speciality once you get to step 4 of creating a character. This doesn't stop you from creating a character for that speciality, but none of the modifications happen until you can actually pay for them, which occurs in step 4. Once you purchase the speciality anything specifically mentioned to modify or change then occurs. Modification, if any occurs in step 4 when you purchase the advanced specialty, not before.
As applies to the OP issue, Sanguinary priest does not specifically state your apothecary then recieves all of the normal apothecary special abilities, it simply states the priest's special ability is in addition to whatever ability you previously selected.