Hi and welcome!
Do you really mean using only one Mixcube monitor for mono monitoring and not a pair of them being fed the same signal?
You need to take one thing into account if you are considering using the headphone jack as a line output, and that is that headphone jacks are unbalanced stereo and not balanced mono. This means that a single jack has connections for both the left and right channels plus the ground as a return. A balanced jack carries only one channel in positive and negative phase plus the ground. If you were to use a TRS jack lead to connect the headphone output to the Mixcube's balanced input, you wouldn't do any damage, but you would not get much sound out. The Mixcube would amplify the difference between L and R channels in the source, which, if summed to mono in the Duet2, would be small and tizzy.
The Duet2 headphone output can be used, but you need something like an insert cable to split the L and R components. You would plug the TRS end of the insert cable into the Duet2's headphone output and one or both of the TS ends of the cable into one or two Mixcube boxes.
A better scheme is to use the Duet2 break-out cable, as it has two jack sockets that are true balanced. My guess is that the Apogee support folks were referring to taking a balanced TRS output from there into your Mixcube rather than using the headphone output. The break-out cable route works with TRS jack leads, and by using two TRS cables you can take both L and R outputs to a pair of Mixcubes if you wish.