M.2 Slot #2

Solution
No issue because you only have one M2 drive and one magnetic HDD.
There is no "fixing this" because it is a lane bandwidth limitation that all Z270 systems will have

Since you are only have one M2 drive it is a mute issue because you will only use M2 slot number 1
If you did have 2 M2 drives then as long as you only need 4 or less SATA ports it is still a non-issue. It would only be a factor if you needed 2 M2 drives AND 5-6 SATA drives.


With all of that said there is a couple suggestions I would change on your build:
PSU: You want the G2 or G3, the G1 version you picked has long term quality issues
Memory: Paying for anything beyond factory speeds (DDR4 2400) is not "worth the squeeze" on intel systems.
CPU Cooler: An AIO cooler...
That's not an "issue", it's just a warning.

The board has 6 SATA ports.
M.2 #1 can use both SATA and PCIe modes. When populated, you lose the ability to use SATA port #1.
M.2 #2 is PCIe only, and when populated, you lose the ability to use SATA port(s) #5 and #6.

So, you could still populate with 2x M.2 drives AND use the remaining 3 SATA ports for HDDs etc.

In the build you propose, with 1x M.2 and 1x SATA HDD, you're only losing SATA port #1.
Could still use 1x M.2 + 5x SATAs OR, in this case, you'd still have 4x SATA ports unused (yet still fully capable of being used).

https://www.asus.com/ca-en/Motherboards/PRIME-Z270-A/specifications/
 
No issue because you only have one M2 drive and one magnetic HDD.
There is no "fixing this" because it is a lane bandwidth limitation that all Z270 systems will have

Since you are only have one M2 drive it is a mute issue because you will only use M2 slot number 1
If you did have 2 M2 drives then as long as you only need 4 or less SATA ports it is still a non-issue. It would only be a factor if you needed 2 M2 drives AND 5-6 SATA drives.


With all of that said there is a couple suggestions I would change on your build:
PSU: You want the G2 or G3, the G1 version you picked has long term quality issues
Memory: Paying for anything beyond factory speeds (DDR4 2400) is not "worth the squeeze" on intel systems.
CPU Cooler: An AIO cooler does not gain you anything over a high end air cooler. A minute or two into gaming/rendering and the CPU temps will be the same (maybee 1-2 degrees apart at most). Difference is that the AIO cooler has a "shelf life" since the coolant will eventually evaporate (as any liquid does under heat) and it will loose cooling effectiveness, and if it gets low enough it will burn up the pump.
 
Solution
Totally agree with the suggestions BUT:
1. While >2400MHz rarely shows gains on Intel platforms, there's a Team Dark 3000MHz kit available which is actually one of the cheapest 2x8GB kits (of any speed) around.

2. The G3 is a great PSU but, for equal quality and a much cheaper price (with rebates) the SeaSonic FOCUS Plus Gold 650W would be my choice.

PCPartPicker part list / Price breakdown by merchant

CPU: Intel - Core i7-7700K 4.2GHz Quad-Core Processor ($287.89 @ B&H)
CPU Cooler: Noctua - NH-D15 82.5 CFM CPU Cooler ($88.88 @ OutletPC)
Motherboard: Asus - PRIME Z270-A ATX LGA1151 Motherboard ($99.99 @ Newegg)
Memory: Team - Dark 16GB (2 x 8GB) DDR4-3000 Memory ($139.99 @ Newegg)
Storage: Samsung - 960 EVO 250GB M.2-2280 Solid State Drive ($127.99 @ Amazon)
Storage: Seagate - Barracuda 3TB 3.5" 7200RPM Internal Hard Drive ($69.09 @ Newegg Marketplace)
Video Card: MSI - GeForce GTX 1080 Ti 11GB GAMING X Video Card ($774.88 @ OutletPC)
Case: Phanteks - Enthoo Pro ATX Full Tower Case ($84.99 @ Newegg)
Power Supply: SeaSonic - FOCUS Plus Gold 650W 80+ Gold Certified Fully-Modular ATX Power Supply ($54.99 @ Newegg)
Operating System: Microsoft - Windows 10 Home OEM 64-bit ($88.89 @ OutletPC)
Monitor: Asus - VG248QE 24.0" 1920x1080 144Hz Monitor ($246.99 @ SuperBiiz)
Total: $2064.57
Prices include shipping, taxes, and discounts when available
Generated by PCPartPicker 2017-11-20 18:37 EST-0500

Great choice with the NH-D15.
As an FYI (i'm doing it currently), if you want to go for a colour scheme, they do now offer customizable aspects too.
https://www.amazon.com/Noctua-NA-HC3-chromax-black-swap-heatsink-NH-D15S/dp/B076569Y8X/ref=sr_1_8?ie=UTF8&qid=1511220984&sr=8-8&keywords=noctua+swap
https://www.amazon.com/Noctua-NF-A15-HS-PWM-chromax-black-swap-premium-grade/dp/B07654B9MR/ref=sr_1_3?ie=UTF8&qid=1511220984&sr=8-3&keywords=noctua+swap&dpID=41V2HaYM4yL&preST=_SX300_QL70_&dpSrc=srch
 
Thanks a ton Barty, I think I'm going with that final list you put together. Seems very nice and at a great price too. Are those two noctua dh15 customization parts bought separately? Also, is the black and red outer part the only color option? I kinda have a blue and black theme for my pc right now?