What tool head are you using?
In all the slicers I looked at, the assumption is that the z-offset between the two nozzles is fixed at zero. The Lulzbot Dual Extruder V2 can (must) be adjusted to make this true. The Dual Extruder V3 is set at the factory but can be adjusted in the field, see V3 Dual Nozzle Height.
Another possibility is to use the extruder start code to add an M206 Z offset for each extruder to compensate for the difference in nozzle height. M218 would be a better choice but you would need custom firmware to enable the Z component.
Note: The Dual Extruder V3 auto level uses both nozzles (because one nozzle can’t physically get to all four washers). Again the assumption is that the nozzle Z offset is zero. I’m not sure how a non-zero offset would affect the auto level results.