If I install the default button code for the "Ref All Home" button, the machine homes perfectly and the slaved motor remains active however it does not square the bridge. It also appears that it makes no difference what offset I enter for the slaved motor as the the gantry only moves off the homing switches equal to the offset entered for the Y motor ignoring the B motor offset.
I think that you're misunderstanding how slaved homing works. Mach3 only backs off the switch until the switch opens. The Home Offset specifies the location of the switch in machine coordinates, Not how far it moves off of the switch.
In order to auto square the gantry, the switches must be located so that the switch locations are what squares the gantry. If you need to move one side a certain amount, then you need to write a custom macro, as you've found.