I'm looking into this now to find out. I'll update this thread as I get info.
Thanks Tait, appreciate that.
In the end it's EA/BW's call how they want to implement it, the items do even have a different icon (the star-like icon instead of the Cartel Coin icon), but honestly, to have them work one way for two Rep factions and then change on the third... well, even if it was initially a bug I think you'd want to take a serious look at whether this may be a genuine disservice to your players at this stage.
Especially given, as others pointed out, that the items can still only be acquired via CM packs (albeit indirectly) through grinding Rep Items and Cartel Certificates, since both are only obtainable through the Packs. Again, even if it wasn't your original intent to have them unlock, given how things have played out, it's probably worth a good hard look.