With automatic bed leveing your z home position is at top. So after homing you have a working coordinate system. The error is small enough to stop shortly above the bed. Version 0.92 will go down on it's own if you are starting too high.
Depending on printer it might by easier to skip z homing and do a z-probe like you described. On other printers that may damage your z probe if you start too low because activating z probe is not possible at starting height.
You can use G30 to set Z by a single probing at your current position. So you can achieve your propsed behaviour by
G28 X0 Y0 ; Needed for correct positioning
G1 X100 Y100 F2000 ; Center position
G30 ; replace Z homing by probing
G32 ; Recompute rotation matrix