welcome to the forum!
A disclaimer to begin with: I have never used the ilastik knime node other then to confirm that it is working. I never use knime, so I am not an expert on this at all. But for the ilastik part…
Since the output per default is a probability map, you could also think about thresholding the channel you are interested in to get a segmentation (if you are only interested in a single class). If you want an image like the simple segmentation you could also get it by processing the multichannel probability map and always select the class with the highest probability per pixel.
Another possibility is, as you already mention, calling ilastik not using the ilastik knime node (have never done that). ilastik has this headless mode that allows calling ilastik with a trained project file on new images and setting all options as command line arguments (for the export source you’d pass the
--export_source="Simple Segmentation" command line flag. For the bit of outputting an image column from files (ilastik will write to files) and display it in knime, you should probably search/ask in the knime forum.
Hope this gets you started in the right direction.