This is amazing news. I currently have to run 2 Jekyll installs to do what I want with custom post types (before this I had a fork to add a different type and that was getting hard to keep updated): I have one main Jekyll install for my blog, and inside of that inside /photos I have another Jekyll for my photo blog so I can do things like this:
http://paulstamatiou.com/photos/japan/two-weeks-in-japan/
<3 open source! All hosted on S3/CF with https://github.com/laurilehmijoki/s3_website