How have you configured the M-code?
I would think you need to set it to Exec/wait/sync, so it waits until homing is finished, then re-syncs the interpreter.
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The ToolTableSet.c has the barebones for getting/setting the values required for setting the tool length. And here's a copy of what I use on my lathe for setting the Z (which I do by touching of the end of a known length of bar, but also includes the option to use an offset)- #include "KMotionDef.h"...