Move the MegaZero filament holder to the side rails.
thingiverse
I thought about putting the Mega Zero in an enclosure, but to do that I had to keep the overall height down. Then I looked for a place to relocate the filament holder and thought the rail on the left was suitable for it. You may be worried about the interference with the Z-axis motor, but as far as I've tried it didn't get caught in the filament and it when the roller moved to the top. If you are worried, recommend replace the Teflon tube with a longer one.
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