Okay... so, I had the import types reversed in my head. Importing as "Composition", will force the bounding box of every layer to fit the width/height of the comp itself. Importing with "Composition: Retain Layer Sizes" will actually crop the bounding box down to the layer's content.
I thought retain layer size meant that it kept the size of the canvas, regardless of transparency in the layer.
Still, it would be nice to know if there is anyway to address that scenario in AE....
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As you have already discovered, the native size of a layer's bounding box is defined at import by the means you choose to import. To reduce the boundaries of a layer after import, you use a mask. To increase the boundaries, apply the "Grow Bounds" effect.
Thanks Andrew. I didn't realize that a mask would actually provide a new bounding box for the layer itself. That works too! Bingo.