All the other local connecting flights you see are franchise flights, so cannot be used with the 2-4-1 voucher. However, they tend to be quite inexpensive, so you can just pay cash for those on a separate booking.
If you call up BA and book it directly over the phone with them they can put all of your flights together on one booking, which really makes it easier! My dad had his JER-LGW flights in the same booking as his BD LHR-BEY flights which he took a few days ago.
