it does not really. you just have to be sure you don't plug a sata drive into the disabled port. they are numbered so its easy to accomplish.
other than that, there is no problem as this is a normal thing for motherboards to do. the manual will tell you what gets disabled so as you're putting it together you can avoid that port.
you can save a ton of money going with a ryzen chip vs that expensive intel one. you'll save on the motherboard and cooling and then some. can knock a few hundred off the price as well by dropping that ram some. 64 gb is overkill for only a couple uses. i see hundreds in savings easily.
and 500 gb of ssd is nowhere near enough either if you don't have other options already.
here's one thought that adds more storage and drops down the overkill stuff some. leaves room for whatever cooling you want though it won't need much more than a $50 air cooler and that's more than enough. saves about $300 and gets a lot more for the money.
PCPartPicker Part List
CPU: AMD Ryzen 7 3800X 3.9 GHz 8-Core Processor ($329.99 @ B&H)
Motherboard: Asus TUF GAMING X570-PLUS ATX AM4 Motherboard ($174.99 @ B&H)
Memory: G.Skill Ripjaws V 32 GB (2 x 16 GB) DDR4-3600 CL16 Memory ($139.99 @ Newegg)
Storage: Samsung 970 Evo 1 TB M.2-2280 NVME Solid State Drive ($179.99 @ Amazon)
Storage: Western Digital Blue 4 TB 3.5" 5400RPM Internal Hard Drive ($91.99 @ Adorama)
Video Card: EVGA GeForce RTX 2080 SUPER 8 GB KO GAMING Video Card ($729.99 @ Newegg)
Case: NZXT H710i ATX Mid Tower Case ($169.99 @ Amazon)
Power Supply: SeaSonic FOCUS Gold 750 W 80+ Gold Certified Semi-modular ATX Power Supply ($109.99 @ Best Buy)
Total: $1926.92
Prices include shipping, taxes, and discounts when available
Generated by PCPartPicker 2020-07-24 18:28 EDT-0400