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Answering my own question: The definition file (on Mac Cura 5.0.0) is at /Applications/Ultimaker-Cura.app//Contents/Resources/share/cura/resources/definitions/ultimaker3.def.json. This file needs to be opened with a text editor and the line "nozzle_offsetting_for_disallowed_areas": false, added to the "metadata" section. This will allow the second extruder to print to the same area as the first extruder. Additionally you need to make sure Print settings --> Build Plate Adhesion --> Build Plate Adhesion Type is "None" (even if you have disabled adhesion in the recommended settings). By default the disabled value is "Skirt" which still prints a skirt of both colors around the entire print object, which would go outside physically possible range. Check from the preview that no rim is printed. Unfortunately just disabling the build plate adhesion type was not sufficient, the definition file had to be modified also. 😞

I'm printing a two-color design with an Ultimaker 3. When I import the two STL files and set them both to extruder 1, both models fit in the print area. But when I set the second (much smaller) model to use extruder 2, the gray unprintable area expands and the first model can no longer be printed, even though it uses extruder 1. The smaller model using extruder 2 is within the extruder 2 print area, so physically the printer is able to print it, but Cura is preventing it. How can I make Cura understand that the first model can be printed, since it is within that extruder's print area? I read about nozzle_offsetting_for_disallowed_areas flag, which apparently allows Cura to print within the gray areas, but I couldn't find the Ultimaker 3 definition file. Could someone point me to an Ultimaker 3 definition file with this flag enabled (or second extruder area limits removed)? Below is a visualization of the problem:

Finally found the settings that control these: Remove Mesh Intersection will prevent overextrusion by removing the overlapping parts. Alternate Mesh Removal controls whether one (apparently arbitrary) model is printed or whether both are printed by alternating layers (to make the bond firmer).

I understand that to print with two colors you need to load the model as two separate designs and assign both models to a particular extruder. What I couldn't find anywhere is whether the two models can overlap each other or whether they must be complements of each other? It would be much simpler if the models could overlap and Cura would handle the rest rather than having to handle it during modeling – useful for example for adding text to some object. If the models can overlap, which extruder is picked for overlapping parts? I tried a quick test using two boxes, and it seems that the overlapping parts are filled 100% with alternating colors. 😳 Can this be controlled somehow?