Unfortunately you seem to have hit an edge case with a third-party upgrade that didn't work with the new file system, APFS.
While Apple should probably sell a boot drive upgrade themselves, every time you install a non-standard part there's a small risk of incompatibility, immediately or down the line. It's not really the third-party SSD manufacturer's fault, because APFS hadn't been released when that drive was released. It's good Apple were able to eventually help you, but there's always a risk, and you got unlucky.
I don't mean to sound flippant — I've had similar issues myself! I've upgraded boot drives and GPUs in my (older) Mac Pro, and while they usually worked OK, there are lingering issues. For example, I don't have a boot screen with my third-party GPU, so I can't use recovery mode or easily boot to alternative drives, and I can't return to the original GPU because a colony of ants made a home there. Infested with bugs, for real. :)
These days, I mostly focus on external upgrades, which are faster and cheaper than before. To avoid further issues, you could buy an external Thunderbolt enclosure for your new drive, pop it in there, then reinstall the original boot drive. You can then leave the external drive permanently connected.
The new Mac Pro might have the same limitation regarding the boot drive (not sure yet) but at least you will be able to install additional internal drives (via PCI) rather than replacing the existing drive. Apple have listened to pro needs, and the new system will be far more open to upgrades. It took a while, but the situation has improved.