I assume that challenges like the following are solved:
- privacy regarding shipping
- transfer security regarding intermediate code
Glacier protocol basically vets the hardware that you use for it in order to ensure it's 100% clean. A dishonest manufacturer will obviously not use clean hardware to generate the BIP38 keys but it doesn't matter if you only give them the intermediate code because they don't know the BIP38 password for it.
Then again, a dishonest manufacturer wouldn't impose such a restriction on itself in the first place and would just ask you for the password to generate a key from.
An honest manufacturer will usually take bigger steps than using laptops with removed parts in them as Glacier says to do, and build custom boxes that don't even have these parts in the first place, wipe the disks after each batch of keys is made, and so on.