Try exiting the unit design screen and re-entering, or saving and reloading.  This happens quite frequently with not only various articles of equipment and clothing, but also traits.

I don't understand this

While I agree, I hardly ever get to lategame warfare technology either, but I do use chain-mails on a lot of occasions (I usually focus research highly).

Sincerely
~ Kongdej

Has your custom race the Heroic trait? If yes, that may be the reason. It removes access to the leather cuirass. Also, Leatherworking does not grant access to any cloaks.

Edit: Okay, I took a look at your save and your faction does have Heroic.