Someone already made this improvement for FlatCAM. Unfortunately, as with some other big improvements (like 3D acceleration for the canvas, drill path optimization), it didn't make it to the official release. The solution for you might be to do what I do: I customize my own version of FlatCAM integrating into it things that I find useful (like above mentioned optimizations, some GCODE drill procedures that duplicate PCB-Gcode ULP from Eagle, generating negative SVG's and so on).
Marius, do you have any pointers to who has implemented rest machining? I would like to also make a custom version of FlatCam with that feature.
I may have spoken around the question in the previous answer. I don't know about "rest machining" but in the previous answer I meant that there is a FlatCAM function to clear the copper outside the PCB features, using multiple tools and it is done exactly like OP said: "We could generate G-code with bigger tools for main isolation routing, then subtract its geometry from isolation area and use small tool to finish the job thus saving machining time and tool wear." It was originally introduced in the fork of Denis Hayrullin: https://bitbucket.org/Denvi/flatcam/src/master/ It's the same fork that I've used as a base for my FlatCAM fork for which I post the results (Nightly installers) in the topic below.