I have certainly seen some trickery done by refurbishes/resellers. I would assume your Activation lock bypass theory is correct. This could be any number of things, people are always trying to find new methods to get past locks which would prevent use of the device.
As for how the change was done, or how it can be redone, I don’t have a definitive answer. Those sorts of bypass methods often not permanent (as you have discovered). And are sort of inherently seedy. There’s not anything wrong with that, but there’s only so much risk I am willing to endure myself or for people I fix for. I personally just don’t like using tools which involve that sort of thing from sources I don’t know, or trust. So I tend to steer away.
There are reprogrammers which can be purchased, but these generally require components (usually the NAND storage) to be desoldered from the board to be used. And in some cases jailbreak can bypass. At this point, you have little to lose. I am not sure that either of these places will have answers, but there’s lots of good info at the [link|https://www.badcaps.net/forum/index.php|BadCaps forum|new_window=true] and [link|https://logi.wiki/index.php/Main_Page|logi.wiki|new_window=true], although much of the information there is highly technical so proceed at your our risk.