When using tree, and using a recipe which uses a GT machine, its model does not appear in the tree.

By hovering it you can see the name but not the icon/model of the machine

This appears to be an EMI bug that occurs if the batching renderer is disabled. Rendering of the GT machine is triggered by

as it is the category for the recipe.
The overload of StackBatcher.render which is called here (the one accepting a Batchable) does not appear to fall back and render the Batchable manually if batching is disabled, unlike the one accepting an EmiIngredient. This causes the machine to simply never be rendered.

This is a correct diagnosis, weird, thanks.

From my understanding this is simply the gregtech machines being rendered inconsistently with vanilla items and something they would need to fix, I believe they have a bug open.

This is probably fixed in the latest release since the code now checks for StackBatcher being enabled.