Hi again, thanks for looking!
I have now found a way around this.
First, I generate the SD and HD versions of the bitmap atlas using GlyphDesigner.
Then, I note the size of the SD bitmap font atlas (in my case, 128 x 64).
I then created a blank/solid colour PNG in Photoshop that was double that, eg 256 x 128, with the SAME NAME as the bitmap font atlas.
I add THAT PNG to Texture Packer, check the box AutoSD and generate the texture atlas.
This then gives me an SD texture atlas with a coloured box exactly 128 x 64, a perfect fit for the SD bitmap font atlas! So back into Photoshop, I edit the texture atlas PNG and copy/paste the bitmap font atlas over the container box. Now my bitmap font atlas is exactly where the texture atlas expects it to be.
Back into Texture Packer, I remove the containing box again, add the HD font atlas and UNCHECK AutoSD, and just generate the HD texture atlas by itself.
I now have my two texture atlases.
Phew, works a treat though 🙂