orientation seems to matter, and causes either no issues or different issues

Smells like alpha blending is being enabled somewhere instead of alpha testing.

I assumed this was related to #400.

But if not, this is where the lack of pushAttrib hurts. Rendered items can also change state.

Probably not related. I don't see the item counts here.

What gives it away is the rectangular "empty" area around the botania flower. With alpha testing, any pixels that don't pass the test are discarded, which means they never get to touch the depth buffer. With blending, even if the pixel has a zero alpha value, it still gets to touch the depth buffer, which means the depth buffer will have an "image" of a rectangular area around the flower, causing any pixels that would end up behind it to be discarded.

Oh dear. It looks like a bug in Minecraft.

RenderItem.renderItemIntoGUI enables both alpha blending and testing, but only disables testing.

Well at least I can work around it. But same idea to the above. It's harder to police state so that any arbitrary entity will continue to see a "clean" environment.

This should be fixed in 3.5.17.