In my opinion and experience, majority rules plain and simple. None of my 55s need the gear from the bonus boss, so I am generally ambivalent.
That being said, a group really has to make a concerted effort to not get the kills necessary for doing the bonus boss (lots of non-combat CC so trash can be avoided); Usually spending as much time avoiding as it would take to just kill the trash in the first place. So the only time you are really saving is the 3-5 minutes killing the bonus boss itself.
I think it depends on the FP. MR bonus is simple, but if you have arch you can speedrun Athis without the bonus.