You are only using a portion of the battery to run a 12V system. If you are only charging at 12V, you are getting shit for voltage anyways. Even charging the 16v post at ~17.5v-17.8v, I am only seeing 12.1-12.2v on the 12v side.
That is how it will be due to how that battery works..... the 12 volt post on the battery is only using part of the battery, only some of the cells, to supply 12v. Then all of the cells are used to supply the 16v. The alt is supposed to be keeping the voltage up on the 16 volt side, so your 12V side gets charged, although weak anyways. You are only charging certain cells and seeing a higher voltage, while the rest of your battery is neglected. They are designed for 16V application.
But what do we know. Why don't you just ask your 'experienced' buddy rather than telling us we're wrong?