"The motherboard M.2 slot #0 shares bandwidth with a SATA Express port. When the M.2 slot is populated, one SATA Express port is disabled."
No, it doesn't say that the SATA 3 (6.0 gbps) port is disabled. It's referring to the SATA express port. Also, it would disable 1 of 3 SATA Express ports. Honestly, I've never used SATA Express, and I don't fully understand it, so I'm not the right person to try to educate you about it. You'd be better
served by Googling it. I pasted a few results below. But whatever you find, it's not a big deal going with the 2.5" model instead of the M.2 form factor. I just think the M.2 is a lot cooler, and neater looking in the build.
google query: sata express vs sata 3
google result:
http://www.legitreviews.com/what-is-sata-express-and-why-it-matters_140093
google query: sata express
google result:
https://en.wikipedia.org/wiki/SATA_Express
PSU: Yes, I'm familiar with that model. There is a great review of it on JonnyGuru:
http://www.jonnyguru.com/modules.php?name=NDReviews&op=Story&reid=454
Be aware that it's semi modular, so there is one cable permanently attached to the power supply; the motherboard power cable.
GPU: Absolutely nothing wrong with opting for the R9 390. I've never owned it but I've read good things. I've not heard that free-sync is better than g-sync, but I will say that many of the free-sync models of monitors are less expensive than their g-sync counterparts. The X34 predator would be a good example.