I suspect that HP are responsible for this. They went through a load of apps, checking that they work on the TP. I reckon that they added/enabled a flag somewhere in the app itself that affects how it is displayed on the TP. This would not then be a GLB bug, but a feature that is added once HP have it. This would explain the differences between a normal .IPK and a downloaded .IPK.
I would raise this issue over on the Dev forums. Maybe info they provide can enable GLB to do the same for apps destined for the TouchPad.