I like the liveries on the ships but I think the un-livery ones should be included as well. At least in SO. The old Diamondback and Black Widow squadrons don't really exist in SO, since you're on the Cerberus. There's also many more "loose" Confed ships not part of your homebase that aren't in those squadrons either but fly those ships.
There should be two sets of MATs, one for WCP, one for SO. The "generic" confed mats should still exist in SO. This bug is logged.