Apple has said no time and time again to free repair of gear that has aftermarket ssd's or hdd's inside of them .
From OWC link you give;
"...While OWC cannot guarantee the actions of the original manufacturer, we encourage our consumers to familiarize themselves with all the right information, including:
-Machine specific information from original manufacturer
-Upgrade specific information from OWC (check out all the useful data on the product page check them out:
http://eshop.macsales.com/shop/internal_storage/hard_drives_and_SSD))
-OWC upgrade install instructions (watch the install video all the way through, don't worry it's short!
http://eshop.macsales.com/installvideos/))
-Expert OWC tech support (Contact us
http://eshop.macsales.com/Service/contact/, if you have any additional questions after reviewing the video! we promise to help!), and
-Your consumer rights per US law and regulation...."
This has been posted due to many turn downs of repair by apple. If you want to do an upgrade and want the warranty to stay in effect be prepared to return the machine to stock.
For instance the base mac mini has 1 hdd option a 500gb hdd . No other option can be purchased directly from apple as they are not offered. So if you put in something different other then a 500gb hdd (a 256gb ssd) and insist on an apple repair under warranty for the t-bolt port 5 months later. They will say you had a 256gb ssd in the machine and it broke the t-bolt port (f- you no free fix) if you think you can beat them in court in that case good luck.
Now if you had the mid mini and put in a 128gb ssd along with the oem 1tb hdd and made your machine have fusion just like apple sells in that make and model maybe you could win.
I could tell you a secret never buy a new mac mini from apple if you plan to upgrade it. Buy a refurbished .
why? they don't always have the parts listed. many times they come with extra upgrades. So if your machine was a refurbished you can say that is what you sent me. A mini with a 256gb ssd.
I am not a lawyer so I could be wrong. but just turn it back to stock and no worries