My setup has the recipe book to the side and an index to the right of it, like this: (ignore the resource packs and mods)

The problem is, the EMI doesn't make it so that the GUI is always centered, making it look like this: (again, ignore the resource packs and mods)

And changing the margins just squishes the sidebar, like this:

So it would be really nice if the GUI was placed in the center, so that I don't get bothered by the fact that it's asymmetrical.

I know you said ignore the other mods and RPs, and im not saying it shouldnt be centered on the search bar. But i do find it rather hilarious that the gui being off center is bothering you yet you have resource packs making the player crafting grid line up 2 pixels low and 5 pixels right of your inventory, and your armor and off hand slots are also egregiously misaligned lol, but its the asymmetry of the search bar causing bother here. (i say this all mostly in jest haha, your bother is valid i just couldnt help myself and not say something)

Anywho, im like 72.987% sure it's the recipe book pushing the whole inventory to the right here? Maybe not the solution you're looking for, but did you know EMI can replace most of the recipe book functionality including craftables? I have a feeling if you add a craftables panel on the left side and close the recipe book everything will align again. This is the first time ive seen the search bar not aligned with the inventory(when set to centered, ofc) and ive used EMI in many different GUIs but i usually have the recipe book disabled so i wouldnt have ever opened it there.

Boo is right here, what you want is EMI's craftable sidebar on the left. EMI only provides minimal integration with the recipe book since it comprehensively replaces it with its craftables.