Check out how the sky textures are defined in the IPK3's "textures.doom2" etc. WadSmoosh renames the doom2 sky textures from sky1 to rsky1 (the same as their patch names). If you're comfortable editing a copy of your HD texture pack (I'm not too familiar with those) you should be able to rename them so that the skies are the names WadSmoosh is expecting, and thus have a WadSmoosh-compatible version of your HD pack.