When an armor stand has a stained glass pane on it's head, it renders fine in vanilla, but the moment you apply a custom model to move it further down, the armor stand's parts that are behind a semi-transparent texture will render behind the whole model, rather than only that texture.

Fabulous graphics settings are being used.

Command used:

/summon minecraft:armor_stand ~ ~ ~ {Tags:["me"],ArmorItems:[{},{},{},{id:"brown_stained_glass_pane",Count:1b}]}

Discovered while testing MC-210584.