Just a little update for those interested. Two more printing plate variations have been tried out - one with the design slightly embedded into the plate, and one with the design extruded quite a bit (about 1/8") from the plate.
The shallowly-embedded plate worked out fantastically well. The embossing produced from it was very crisp and well-detailed, and the filament lines were surprisingly smoothed out. If you're going to try to replicate this experiment, definitely go with this approach over extruded your design - the greater surface area helps the plate withstand the pressure of the printing plate much better.
The extruded plate had a much different embossing result than the shallow one - very large 'pillows' of paper along the edges of the features, which may or may not be desirable. As we expected, the smaller features were not able to withstand the pressure from the press, and broke off. We may try this one again and adjust the press differently, but for now, the extruded variation doesn't seem ideal.