The output/merged_space.ill file is the final "merged" building result. It's an 8760 schedule of illuminance for the whole building, and in the case of models with window shading controls, the values in this file reflect the individual window group shade positions. The .ill files found in the maps subdirectory are the illuminance schedules for the individual spaces' illuminance maps, with a header telling you how to reconstruct the map, should you wish to do so for visualization purposes.
The output/merged_space.ill file, when paired with the numeric/merged_space.map file, has all the information you need for a visualization of the data; the former has the illuminance data for the whole building for the whole year, and the latter has the corresponding 3D point data. Unfortunately--and this is a big unfortunate--the point data does not have space or thermal zone metadata with it. Again, the .ill files found in the maps subdirectory are organized by space, but you have to look at them individually, and reference the header for the spatial construction of the data.
Ideally, these data formats would be improved and a visualization tool would be included with OpenStudio.
