Two parts of different size have same volume when stored.

I guess tweaking scale is done by right clicking on the part from the editor ?
If so what I can do for that is enabling the part dragging of any part in the editor scene (instead of only the parts in the left panel). This way you can attach a part on a ship, tweak scale it and drag it in the container. Hopefully, current state of the part will be saved.

Would be great! I've been using a workaround, snapped scaled parts on ship and dragged them into container during flight. The current state of parts is saved, they are scaled when I take them out. But KIS currently doesn't calculate the scaled volume and mass, all scaled items have unscaled values when stored.

Added part dragging of any part in the editor scene for next version (1.0.1).
About unscaled values when stored, I need more information about how tweakscale resize parts. As mods compatibilties is not priority right now, please open another issue if needed.