What makes my mod great is that it separates the ammunition (weapon ammo, rockets, and heavy artillery). It puts each on a separate line. It's not funny; AAI used to keep these in the logistics tab and the top tab within the transport tab. I moved the AAI versions to the bottom line in the transport tab. (I haven't played for a while, so I don't know if they fixed it after I left.)
I don't maintain the mod. But the process you mentioned is easy; you can do it yourself. Go to the prototypes section in the mod file.
Open entity.lua with notepad.
Change the subgroup line. Press F5 in the game to see which items are in which subgroup. Then save it in the subgroup section of Notepad wherever you want to place it, and change it.
subgroup = "ftl_transport", line 65.
The entire relevant section:
type = "item-with-entity-data",
name = "ftl_ships_" .. name,
icon = icons .. name .. ".png",
icon_size = 64,
subgroup = "ftl_transport",
order = order,
Just replace "ftl_transport" in the subgroup field with the subgroup name of your choice.