What CAM software do you use with your setup?
There is a tool change macro in Chilipeppr and I believe in cnc.js as well,
I have never tried them but perhaps they would give you some hints.
Google finds lots of hits
I assume you have studied this wiki page https://github.com/synthetos/TinyG/wiki/Coordinate-Systems
Not understanding exactly how your machine is running and aligning tool position with work piece, its not obvious how shifting coordinates would do what you want, but you believe it would.
I have to assume you are generating your own Gcode, since the detail of how coordinate systems would affect your design would seem to be custom.
The wiki reference above describes how to change coordinate systems on the fly. The CAM systems have example of how to stop running Gcode to make a toolchange. Seems like a custom combination of the techniques could achieve what you need.
A lot of assumptions on my part. Any of them help so far?
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