dactyl-keyboard
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Manuform: changing only "Center of the curvature for the column" can clip bottom of model
Changing "Center of the curvature for the column" from Pinky finger's column
to Middle finger's column
can clip the bottom of the model.
You can manually account for this by increasing the "Height Offset" from the value used in the top model of 6mm, to 12mm to remove all of the clipping shown in the bottom model.
Perhaps a warning dialog when changing this value from a vertically higher column (pinky, index) to a vertically lower column (ring, middle), with a suggestion to add 4-6mm or more of height offset would be good enough for now.