Inconsistency in transparency of GUI PNG files - only some can be transparent + hover-bugs

When I created a transparent GUI resource pack module, I noticed that only the creative player inventory GUI could be made transparent (minus one tab which always stays opaque), not so the Survival Inventory player GUI, and all the other GUIs though; hotbar, health and hunger bar and options/menue can be made transparent, XP bar again not although it's on the same GUI PNG file. Boss bars can be transparent. Health bar of mobs you ride can be transparent.

There are also inconsistencies occurring whilst hovering over empty or occupied inventory slots, e.g. when a potion or beacon are in effect: Hovering over the inventory, or skimming through the tabs in the creative inventory make the transparent effect field go opaque again.

Placing armour in the armour slots make those "below" the inserted armour slot go transparent, from opaque. Hovering over empty armour slots make those "below" it go transparent. Hovering over the 8th and 9th hotbar slot make the shield slot go opaque. Inserting a block or item into your Survival Player crafting grid make the armour slots go transparent.

Demonstration incl. vocal explanation by the provider of the attached test resourcepack for GUI transparencies, Acrobaticon, can be seen here: https://www.youtube.com/watch?v=UKQHesEOWzw

As he recorded with Optifine but I know that everything he shows also happens in 100% Vanilla, I've also made a quick (non-vocal) demo video in 16w43a Vanilla which can be seen here: https://www.youtube.com/watch?v=YCKLGeyCdoE to make sure this bugpost won't get closed due to him using Optifine in his demo video. I also attached a few screenshots.

The best outcome would be if one could set all GUIs transparent, as this would give mapmakers more flexibility and chances for better immersion of the player with a custom resource pack.

I recall there was a hover-bug in the player GUI whilst hovering over a custom skull (not a Minecraft skull): MC-94576 maybe it is partially related to the mentioned hover-bugginess with transparent GUIs. The fixed bugpost also mentions rendering of the potion effect display like it's still happening as you could see in the example videos with transparent GUIs.

The attached test resource pack can be used in Minecraft 1.9+ (for 1.11 ignore that it shows up "red" and load it anyway).