I'm actually surprised it seems that discs are put in cases by hand. I had always assumed that it was done mechanically in the factory they are made. At least I think that CD's are done that way.
I haven't checked the discs for my Zavvi set yet, but I have to agree with the point about the box as well. Major disappointment the material they used as it literally picks up every mark and finger print possible. - Did absolutely no one order prototype versions before having everything made? baffling.
Most duplicators have workers which put the discs in by hand for any non-standard packaging (i.e. anything that is not amaray or standard-sized two-plates digipak). The versatility of packaging designs for home video products just makes it impossible to have it fully automated especially since the production batches are low. This is no book printing, where the quantity is often in the tens of thousands.
As for the surface picking up finger prints, there are a lot of nobles cardboard coating (as in, artwork sticker which covers the raw cardboard) which may. The soft-touch paper is one, for example. I wouldn't blame them for that point specifically as special coatings can provide amazing visual experience / quality.
Like a few people have mentioned, there's no way the second patch will change the packaging, if indeed we are using the same materials. Even without Christmas, that kind of thing will take months to organise and schedule time to replicate. It was the same situation for Gurren Lagann, back in the day.
Speaking of which, I'm beginning to wonder if there's literally no way to making multi-disk trays like this without there being some issue, at least in Europe (maybe America has the means to do it better). I like the idea of the plastic nubs better than glued-on trays, although it still doesn't appear the issue of loose disks has been fixed. More annoying to me personally is how rough and untreated the cardboard seems to be. After all these years I really would have hoped there were polished systems in place for these kind of releases.
I think they split the delivery simply due to factory constraints and paper shortage. Most elements are probably ready (as splitting the printing in two batch would increase the costs) but to be on time for christmas, they could only prepare a subset of boxsets. That is fairly common.
Regarding your second point, the
French & German release of Kara no Kyoukai by Kazé uses a strictly identical attach system and it is very well made. The ten plastic nubs (made of high density foam) are perfectly centered in each circular spot and the discs are firmly held in place.
There are some drawbacks tho. Every time you press this foam, it gets very slightly bent to the point it keeps surface folds. That means it gets damaged somehow every time you remove or insert a disc. So in a rather long timelapse, this will probably show issues. The second one is related to the fact that is is just some foam sticked to the cardboard surface. If you're not careful or the glue on the nubs is not so good, they can fall off. Oh, and the discs gets scratched more easily because their surface are directly in contact to the below surface as well as dusts.
EDIT: I'll add that there are alternatives to high density foam or standard plastic digipak trays which are much better to hold a disc on cardboard.
Here is an example. The disc (well, its inner center which does not hold data) only touch the small plastic surface at rest. It has much less chance to be scratched. Only downside is the apparent glue. A non-transparent piece would solve instantly this issue.
