It all depends on the room and budget. If you describe your space, design, screen type and screen size, budget, etc. one way or the other could make more or less sense.
It's tough to say... "Yes, way A is better than way B" without knowing the context of the project and your goals. There are some incredible in-ceiling LCR speakers and there are some also-ran look alikes from companies trying to peddle speakers.
If given the option to do whatever I wanted in my own fictional room, then I would say the traditional LCR layout is best. BUT, if that would cause aesthetics of the room to be altered or would cause installation issues THAT'S when I would start to design alternative layouts (like a traditional L/R and an in-ceiling center, for example). Feel free to describe as much as you can and I (& prob others) will make recommendations!
As an example, I would recommend this to anyone looking for a top shelf in-ceiling LCR system: LINK I CAN'T POST UNTIL I HAVE MORE POSTS
BUT.... This is actually better and litterally 1/2 the money ($1500 for all three where the in-ceiling from the same company is $3,000 for 3): ANOTHER LINK
The difference is: One is designed for a special application/install and the other is a traditional, straight forward design. What's funny is that the $500 PD-6LCRi linked above is a much much better speaker than the model "above" it, the $800 SA-200. IMO it is one of the biggest values in speakers today.
Hope some of this helps!