First layer Z-offset in G-code
I don't understand the reasoning behind a first layer having a different offset from the following layers, but, You can manually add a re-definition of the current height after the first layer, suppose your first layer is 0.2 mm, you just need to tell the printer to move to a slightly higher next layer to redefine this as a different Z-offset.

From a G-code file find the start of the second layer:G0 F600 X141.541 Y109.467 Z0.37
Modify this to:G0 F600 X141.541 Y109.467 Z0.42
Now insert the following command:G92 X0.37

Now it is like you have changed the Z-offset.
The reason for not using M206 is that is applied onto current offsets, if you accidentally save setting to memory after printing, it stores this offset. You can use M206, but use it carefully. A re-definition of the Z level is never stored, the next G28 erases the effect, so does repowering the motors.