Kinda the same thing, but flatten will create a series of regions, as chosen by you when comping. Flatten and merge will do that, and then create a single file, merging the regions.
Flatten and merge is a quicker way to end up with a single, edited file. I don't use it, especially on vocals, because after flattening, I would always want to go and check the edit points, maybe adjust the position of some edits to make sure there were no breaths split in half, make some crossfades longer than the defaults, and maybe even to move some of the regions to improve the timing of the performance. Your opportunity to do this is lost once you have flattenned and merged. I might merge the regins manually (using the glue pen tool) after checking and adjusting them, especially if I am going to export the file to melodyne, or some other tuning software.
Thats's just how I do it.