#I'd actually like to use Yukon but I

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ancient cargo
#

Yukon doesn't easily lend itself to being a sub-controller
Why not? It's just a micropython uC with a bunch of peripherals on a well-designed base board. You could follow the same approach as on Turtlebot3 = Rpi connected via uart to a uC board (that would be Yukon).
Do all the (near) realtime stuff on the uC and high-level logic on the Rpi.