Axl, I apologize if I somehow offended you, please understand that it does seem strange for any company to go against something as basic as this.
If you are using LPC NG for your everyday ops make sure the values entered into the MCDU reflect those from the software, if not then have a chat with the pilot (or copilot) and insert the correct values even if these go against company policy, it'll save your butt should things go sour on the day you least expect it.
I'm guessing you fly for LAN?