Yes, that is what I always say. With ditto printing like Stacker does, the bed must be physically levelled.
If I understand right the z probe is on the extruders and moving them y wise outside bed prevents hitting bed on first regular homing which leaves a gap so you will not hit the bed.
At least with current 1.0.4dev version there is a solution (maybe also in 1.0.3 not sure when I added it).
Assuming you make the z probe also z min endstop. You can use
/
Raise Z before homing z axis
0 = no
1 = if z min is triggered
2 = always
This is for printers with z probe used as z min. For homing the probe must be
at a minimum height for some endstop types, so raising it before will help
to make sure this is guaranteed.
*/
#define ZHOME_PRE_RAISE 0
// Distance in mm to raise if required
#define ZHOME_PRE_RAISE_DISTANCE 10
With ZHOME_PRE_RAISE 2 you would then always go up 10mm before doing z probing. You would run
G28 X0 Y0 Z0
and you get the right height. Hopefully z probe is over bed at homed xy position or it will not work. pre raise is only when z axis is being homed (in V2 firmware I'm about to change that behaviour).
Now after 1 row is printed you move to new Y position and run only G28 Z0 and it would adjust z accordingly.
You would use the zprobe for everything without danger of hitting the bed during xy homing and have no need for it.
If that is no doable solution you could write an own command that does z homing just with z probe.