the compatability issue is because that particular motherboard has a feature. That when you are using an m.2 mvme ssd it doesnt allow you to use the SATA port as well, the reason they are telling you is because you cant have the ssd with the hard drive. At least not on the 6gb/s SATA port which is where it should be.. Honestly the big question is personal preference. When you are building your PC there is a million different case options, hardware options, color options. There's a million options. No one answer is better than another.
Scanning over your build i see no issues besides that i would pick a different motherboard that allowed more storage options... like i said though its all on preference. If you like the gigabyte color or company find a different one, but theres a ton of options like i said all depends on price.
and as far as cases go, thats a real personal preference. Alot of new things is glass side panels and RGB lights, but if you dont want that then it gives you more freedom on inside components colors. Also IO, do you need 4 USB ports up front of your case for your phone and everything or will 1 do, alot of things differ from person to person.