Yes... and no.
Seriously, some folks have been able to "get it together" climbing out of the saddle out of phase, whereas others just can't get there. It's one of those things that each team must work through. So, if you're otherwise pleased riding out of phase continue to work on your climbing technique, varying cadance and the like to see if you can find a sweet spot. If after giving your best efforts it just never comes around, then you'll have to make a decision:
a. Riding with one person up and out of the saddle at a time is good-enough and allows us to enjoy the remaining 95% of the time we spend riding seated and out of phase... or
b. There's just something about honking up a hill or sprinting for a county line sign that we can't live without so bye-bye out-of-phase.
Keep us posted on your progress.