I'm working on a speaker layout and am wondering what I should know about this. Does either config work better than the other? Is there an obvious choice as in definitely go one way but if you can't just do the other?
It depends on your room. If you can do ceiling speakers, that will be the way to go for Dolby Atmos, that is what they recommend for their system. Everyone can't or don't want to do overhead speakers, so you have the front height and rear height compromise. If you want go all in on Atmos, do the the in-ceiling if your ceiling is 8 feet (like most ceilings are), if you have a 9 ft ceiling do ceiling speakers, but not in-ceiling speakers. As a last resort, you can use Dolby Atmos enabled speakers.
The Dolby Atmos system recommended speaker placement isn't that flexible, if you are interested in DTS-X, according to DTS, your speakers placement isn't as critical as Dolby Atmos as the DTS-X processor will render the placement of the objects based on whatever type of speaker placement you have.
One thing to keep in mind, we're very early in the immersive audio game, some of the content out there might not be that impressive to you, they still need to tweak it a bit. A lot of the mixes are kind stupid, they do more to pull you out of movie than to immerse you in one. In my opinion, both DTS-X and Dolby Atmos, are kind of flawed in that they recommend too many speakers to be place above your head, however in real life, humans don't really perceive that much sound coming directly above our head. However, some of these sound mixers will place all kind of sounds above you.