The Noctis has an 8 port PWM fan hub that plugs into your motherboard so that you can control your fan speeds in your mobo's BIOS. I wouldn't recommend the Grid or Grid+ because the PWM fan hub in the Noctis is just as good. To answer your other question, the Grid and Grid+ are mounted inside the case on any wall with the double sided adhesive that they come with, not in any bays.
On the topic of the cases themselves, I actually own a White Phantom 410 and will be selling it soon to get the White Noctis 450. When I initially got my 410, I noticed that the window was a bit smaller than I had expected and now I definitely want a case with a bigger window. Unless controlling your fan speeds is a necessity, I wouldn't even worry about the controller. On my 410 I have it set to the max nearly 100% of the time. A controller is only useful if you need absolute silence when your computer is on. It is nice to have, but very unnecessary. In my situation, I am giving up my fan controller and a 140mm fan right next to my gpu for a bigger window and a much better design.
Also, you do not need any 5.25 bays. The only time I ever used my optical drive was to install windows, which could have easily been done with an external dvd drive, like vmem said. If you have a lot of DVDs that you want to watch, get the Noctis and buy a $20-$30 external dvd drive.
Don't worry about having a lot of questions. I did my first build 7 months ago and the funnest part was talking to people about different parts and deciding on which ones to get.