Via usb it wil be detected as a flash drive,so the route will be different. sotrage/sdcard1 is for microSD directly. For external applications use in a usb, try with the folder mount or link2SD. Apps are always installed in internal like in any android device that use unified storage. Also, make sure your usb flash drive is formatted in fat, if it's in ntfs some apps may not be compatible with it.
That applies for legacyrom or stock, since storage is the same in all firmwares