Using 1.3.0 along with a 64x texturepack some armour and tool textures actually increase in size in the inventory. It doesnt matter if metallurgy is the only mod installed or one of many, and its always the same items that get bigger.

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Yes, this is caused by a custom model overwrite that I use to remove the usual 16x16 size limit without changing the relative size of the pixels (see picture). It is not something I we can fix on our side, but it can be relatively easily fixed by overwriting our extended.json model file through resource-pack models, located here.

What you are looking for is basically the whole "display": {, tag removing it (and everything contained in it) will make extended items display exactly like normal ones.