Basically the PHX - LHR fare it seems was considerably lower than the PHX - LHR - MAN fare. It seems to have been some sort of I class special (again valid only to London). When BA price up the change, it works out to 3K more.

This ticket is refundable with a fee, so if anything crops up in the meantime the whole thing can be rebooked, all as one.

The whole thing seems very odd, i'm sure there's a way to figure it out! I think the protection of the ticket (connection on return) is definitely the more concerning aspect of this.