As far as bacteria goes, I don't think it matters. They will colonize any hard surface be it the sand, the glass, or your LR.
And I would have to agree with @Triggreef that what your most likely seeing is just freeing up space so water has a place to flow around the rocks leaving less area for detritus to settle(algae loves detritus), which means less algae and a more stable healthier tank.
And I would have to agree with @Triggreef that what your most likely seeing is just freeing up space so water has a place to flow around the rocks leaving less area for detritus to settle(algae loves detritus), which means less algae and a more stable healthier tank.