I have the same problem. ROMs with hacks, trainers or different regions being in a single archive take up significantly less space. Repacking on different archives means significantly increasing the amount of space occupied.
Inspecting the entire collection and removing unnecessary ROMs is too time consuming task for a large collection.
It would be very convenient to get additional application (as is now done for similar archives) but for ROMs in one archive.
Such functionality is already provided by a number of other game managers, and I would be glad to see it in LaunchBox.