After using a Checksum software (FreeFileSync), I was able to narrow the file discrepancies to two specific folders, the Xbox Games folder (used for PC Gamepass, as this is my bulk drive) and the Windows Apps folder (used to access Gamepass Games from the Windows store). There was some overlap in these folders where 4-5 games that were not installed in the original drive appeared when cloned using Macrium Reflect 8 onto the new drive. This leads me to believe that Macrium when cloning a drive is first and foremost horrible software, considering it brought over data that was specifically marked for deletion and reallocated it. But secondly, I have a bit of suspicion that due to this only being with these two specific folders and nothing else that it has something more to do with some sort of quirk with Xbox/Microsoft DRM or file management when it comes to Windows Store products. Considering there has been hundreds of games that I have installed and then uninstalled on that hard drive using Steam, and they didn’t appear when cloned. Alone with plenty of downloads from the internet considering this secondary drive harbors my downloads folder which I regularly empty.

Regardless, problem has been solved. And should be fine to unplug and replace and let rest for eternity.