Why does my Hugin command-line stitch come out distorted, and how can I fix it?

I think there are two or three possible issues: one with the commands and two with your photos.

1. Make sure you (globally) understand the commands you are running. As you have seen for yourself, the resulting picture is a bit disappointing. Check the Hugin components manual for the different commands, their options and their meaning. For example, you use the -s option with the autooptimiser. This automatically tries to pick a suitable projection. I think this is one of the causes for the distorted result. As suggested in the comments, start with a more basic set of commands, and take it from there. For example, this should be a good start:

    # Generate a project file
    pto_gen -o project.pto ./top.jpg ./bottom.jpg
   
    # Auto optimise (note that I don't include the -s option here
    autooptimiser -a -l -m -o ./project.pto ./project.pto
   
    # Set canvas and crop
    pano_modify --canvas=AUTO --crop=AUTO -o ./project.pto ./project.pto
   
    # Process each of the images
    nona -m TIFF_m -o ./project.pto ./project.pto
   
    # Blend the resulting images
    enblend -o project.tif ./project.*.tif
   

2. I suspect you took the pictures while holding the camera in your hand. As you can see below, I managed to blend the images, but the don't stitch very nicely. This is because there must be a minor shift in the point from where the camera took the first and the second picture. Hugin (or any panorama software) can't correct that. Next time, use a tripod to fixate the point from where the panorama pictures are taken from.

3. It really helps if you put exif info in the file for Hugin. This "metadata" is automatically stored in the image file format by your camera. This includes focal length, which is an important part of the info that Hugin needs to process your photos correctly. Always make sure you use "straight from the camera" images for stitching.

Finally: if you have the opportunity, try the Hugin application (Windows/OSX/X). This guides you through the process and gives you a much more friendly user interface.