
From what I've understood previously, "bonus objectives" were not supposed to be the side quest branches, but scenario-style pop-up miniquests that you get upon entering a certain area - think the eels quest from begining of vash'jir or vultures quest from uldum, only less "questy".
A good example would be bonus objective to miniquests accompanying the main questline - the questline sends you to a wood to gather 10 branches. When you enter the wood, you get a pop-up to kill 10 big bad wolves as well, when you're at it, for some extra reward. The quest about gathering branches has quest text, the miniquest for wolves doesn't, and will remove itself from your log as soon as you leave the wood. I'm not even sure if it would go into your log in the first place, and not just stay as a popup or an addition to the main quest record.