Wanted to post a reply here even though I've been in contact with you by email, just for others who may read this thread.
I did some experimenting with abyss web server, I thought maybe I could make some small code change and fix the problem.
The interesting thing is that it seems that it does actually execute the /Setup/Default.aspx page and it returns a web response status code of 200 which indicates no errors. I added some logging statements after each main step of the process and it logged each step correctly and it appears to have correctly completed the setup process, the only thing it doesn't do correctly is that somehow the page output of the /Setup/Default.aspx page just never gets rendered in the browser so you get no confirmation that it has succeeded and no useful information if it does not, but if you leave it alone for a few minutes to make sure it has had time to do its work, it seems that it all works out and the site is correctly configured. So I tried it again with a new empty database just to be sure and again it worked correctly it just doesn't indicate it in the browser as it should.
Hopefully they will fix the issue but I can confirm that it actually does run all the setup code and as long as the database connection string is correct and the abyss is configured correctly for asp.net it should work for you even if they don't fix the rendering issue.