I have looked at that case, however, user reviews are mixed. A backwards panel would probably annoy me as well knowing that it's backwards. Not to mention, when you include shipping, I believe the case equates to around $50+ USD. Not really willing to pay that much for a case again, with mixed opinions and a backwards print.
For the Tone Board and the Atom, I would say I'm pretty happy with the purchase. I think my biggest gripes (though, not major ones at all) with the Tone Board is the lack of a case and the fact that the led is bright af. You can see in the picture but it can be a bit blinding at night. I ended up putting 5 layers of kapton tape over it to subdue it lol. Other than that, I'm using usb input with RCA out. I won't comment on any audio qualities though as I do not have much to compare it with (and I also lack equipment for proper a/b testing).
As for the JDS Atom, it serves me well. I have a pair of Custom Art's that have a 6.5ohm impedence. The JDS Atom works well (<1 ohm output resistance) as I hear no hissing/ any sort of noise which can be present in high output impedance amps. It also powers my 6xx and is able to bring it up to good volumes. Again, I have no complaints for the amp. The plastic build might be a turn off, but I have no problems with it. It's black and blends in with the shadows anyway. The only issue with it (imo) is that there is no balanced. I know some people like having balanced outputs, but I personally don't need it. If balanced is important for you, then the Atom doesn't have that.
As for the SPDIF, it's a coaxial connector so if you have any devices that have that, you can connect that up. In my case, I have no use because I do have SPDIF on my motherboard, but it's optical. In terms of differences between usb vs SPDIF, you can read about it online, but it all boils down to "Usb or SPDIF, it depends on the systems being used to playback/ send information."