Both teach similar things, but the PRes Navy BMQ-Common has a lot more time to expand on some facets. I do know that if one transfers into the Regular Force, new officers who had the PRes Navy BMQ bypassed the first 7 weeks of their BMOQ, while those with the PRes Army BMQ-Land did not.
A friend of mine did his PRes Army BMQ with me, and then transferred to the Navy about a year later, where he needed to redo his BMQ because it was not equivalent. You may want to check with your CoC to find out if having done both BMQ and BMQ-L SQ will be enough to grant an equivalence if you do decide to switch.