The format connects to internet but yeah, it doesn't update. I think it appeared at the same time as the NNID as 4.x firmware don't require to connect to internet to format (and don't have NNID support).
i have the exact same problem too and my system and emunand are not linked never got the gift bug till i installed 2 jap eshop titles, fantasy zone 1 and 2 and it only hapens to those two jap titles
this is not related to system and emunand being linked it i a seperate bug that is only affecting jap eshop titles(maybe cart titles too?) being installed on different regino consoles
i have a US 3ds and now it's being reported on EU region console too
it'a really not that big an issue, not sure now many jap eshop titles there are that are not going to be released for other regions
but if it's only a few titles it's not a big deal just wait till you can find a cia of the same title for your region and reinstall it and delete the jap version