OK, I've found a way that's not adaptive but cuts out having to create cutouts manually.
By not adaptive I mean that any changes made to the circuit copper requiring multilayer clearance after this is done wont propagate down unless additions are multilayer objects such as through hole pads/vias
It's a rather convoluted process but the result is more accurate than the tracing things manually, especially if the outline is more complex than this example shows
The traces and pads below are not a real circuit and are just for this example.

We then add our polygon pour to the layer containing the traces and adjust its properties/clearances to suite. In this instance we are working on the top layer.

We now explode the polygon to free primitives

The structure has now been converted into a copper primitive, we double click it and change it to another layer. Here its the bottom layer

Double click it again and in the properties we change its Kind from "Copper" to "Polygon Cutout"

We now place a polygon on the bottom layer over this cutout and we end up with this

Now we select this polygon, right click and select "Explode Selected Polygons To Free Primitives"
Each copper primitive is independent now so we select the ones we want as clearance and convert those in the properties->Kind from copper to polygon cutout
At this stage we can clean up by deleting the the first cutout and the copper regions we don't want.

Turn off single layer mode, switch to the layer containing the original traces, select the cutouts from the bottom layer, copy using some reference point on your current layer and paste as many times as you need.
Then transfer the copies to the required layers
If you already have polygons on each layer they should now have their cutouts otherwise add your polygons now
We now have have polygon clearance on all layers for the copper on one layer
