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However, I just ordered an intellijel 7U, and I mocked up some images for a SynthAccess guitar module that should fit in the 1U space, but my image is getting cropped incorrectly. I designed for 44HP an 1U. If I edit the custom module to say that it's 48HP, the the height grows, so I must have the proportions right. However, I never see the pixels at the edges. It's like there's a huge inset, even though the proportions are correct.

There are two "standards" for 1U module dimensions. ModularGrid uses the one from Pulplogic.

Can anyone suggest a method for creating a proper 1U image?

You have to add a small vertical padding for 1U modules that follow Intellijels standard.
Crop the module perfectly, read the height and multiply it with 1.082. That is the new height of the canvas. Center the module vertically in the canvas and save as .png, transparency preserved.

See this rack:

-- rsdio