I printed https://www.printables.com/model/204065-super-low-profile-spool-holder-for-mk3s as it was the lowest profile spool holder I could find.
But I needed just another 2 or 3 mm of clearance, so with https://twitter.com/dz0ny's help in Fusion 360 I cut the length of the arm for around 1 cm, bringing the height down by about 5 mm. The spool now has 5mm clearance from the mounting frame, and 5mm clearance from the shelf above. Yay!
The author remixed this model.