Could a brand new, unused, factory unlocked phone have been rooted?

I bought a Samsung Galaxy S4 on ebay. The description said that it was "Factory Unlocked." It also said that it was "A brand-new, unused, unopened, undamaged item in its original packaging (where packaging is applicable)."

When I received the phone, I found that it did not pass Google SafetyNet. Someone suggested that it might be because it is rooted, so I used a Root Checker app; it said it wasn't rooted. So I downloaded an app called Phone INFO to see if it might be able to tell me anything else about why it wasn't passing SafetyNet.

Interestingly, the Phone INFO app shows "Root Existence: Yes" and when I tap on that, it says "Root INFO: /system/xbin/su". So the phone has apparently been rooted before. It also says: "Knox Warranty Void: 0x1".

I am also unable to update the phone to lollipop (it is running 4.4.2), and the phone will not connect to Samsung Kies or Smart Switch. I am wondering if it may be running a custom rom, but I don't know how to tell. I honestly don't know much about this, and have only understood some of what Phone INFO has shown me by googling things.

Aside from all that, the phone itself seems to be a legit Samsung S4, from what I can tell.

So is it normal for a brand new, factory unlocked phone to have been rooted and/or have a custom rom? Should I attempt to return this phone to the seller, or can I (or maybe someone at Best Buy or something) simply flash a stock rom and it will go back to normal? And if I do that, will it remain unlocked?

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