the benefits of having flush mount speakers are: 1) no comb-filtering from speaker boundary reflection (at least for the boundary the speaker's attached to), 2) no speaker/boundary reflection issues to smear transients, 3) dynamic reinforcement from boundary itself being so close to the driver, for greater efficiency.
Down side to flush mount (considering you have sealed enclosure for speaker, and not wall cavity as enclosure): 1) is you will be reinforcing the bass modes in the room with such a setup, 2) it's likely your speakers won't be able to adequately "aim" or point towards the desired listening positions for proper tonality, due to water-fall response issues, 3) on ceiling mounting applications - as considered here - yes, localization and proper anchoring of the soundstage will be thrown off...drawing you out of the perspective, in relation to the screen. (basically, the dialog will be sounding like it's coming from the ceiling, and not centered near the phyisical screen.
I personally can usually work with ceiling mounted rears and sides, often. However, I don't like front L/C/R speakers up front in a ceiling mounted application. Just doesn't make a realistic front sound-stage, wich is critical.
I'd recommend using the back, sides, etc, but do some sealed boxed speakers for your L/C/R's. I think you'll get better restults, have better flexibility, and a higher overall performing system, potentially.