I'm not speaking entirely from the perspective of someone who just read the corporate line, but as a programmer and a network administrator as well.
For the most part people get the idea that 'saving data twice as often' is equivalent to 'writing down twice as much information'. Unfortunately, that's really now how these types of systems work. Speaking from the technical perspective there's a lot more to consider.
First you have to understand how data is saved which is not always 'we have new data here, write it next to the old data there' but more 'what of has changed that we need to record and how do we organize that data to record' even before going through the process of sending that data across the network to be written to a disk, all of which takes time that increases closer to exponentially than to linearly.
For the itemization, yes it's bad, but it fits into the current schema of how they process this data. If they add a new token that goes into your inventory, it's easier to fit into this schema than adding some new form of storage, i.e. A currency wallet for those tokens. Granted, they very well could add those tokens to the currency tab for seals and such, but they don't want to put you in a position where you've collected a thousand tokens from a 2.x beast tribe that you can't ever get rid of. The current system allows you to get rid of those tokens you no longer needed.
Personally I think they should itemize those tokens in the same way they did crystals, but there could be a dozen other reasons we're not aware of for why they didn't... Likely the whole turn-in system they set up for those is incompatible with the way crystals are stored, though let it be known that the whole 'drag the item here or right click' system was supposed to go away after Beta and never did.
So honestly, it does explain many of their decisions once you realize how that whole 'twice as often' bit affects the system at large and not just the small inventory part you're considering.