Hello, as I understand it, several modifications conflict with 'SkinPort', such as 'Twilight Forest', 'Headcrumbs', upd 'Botania'.

Twilight Forest - Giant Miner.

Headcrumbs - Heads.

Headcrumbs - Human.

Botania - Gaia Guardian's and Head.

I understand that most likely it will have to patch the modifications themselves, do you have any ideas how to fix it?

Regarding TwilightForest (and probably Headcrumbs) the issue is being caused by the mods itself
Here is an extract from the render class for Giant

public RenderTFGiant() {
    super(new ModelBiped(), 0.625F);
    this.textureLoc = new ResourceLocation("textures/entity/steve.png");
}

As you see it uses vanilla's model to render which grabs the unsupported texture.
But I actually found out that you can fix it using RenderLivingEvent.Pre
Here is the Gist, not the cleaneast solution and could potentially break some other mods.
https://gist.github.com/H4kt/8cf101aced9fa39b4b332da6e71a1400

But somehow it keeps breaking the rendering of held item

The soution for skulls might be very similar to this one

Sorry, I don't really want to patch this mod for every incompatibilities...
This mod is licensed under MIT, please feel free to fork it, and make your own patches.

Having a lot of trouble with it too.

These comments will be noted for a fix in Et Futurum Requiem's Alex model.