I want to have one user page and multiple project pages hosted by GitHub Pages but available under ONE custom domain (with subdomains for each GitHub Pages
You can do it. Notice that all DNS CNAME entry point to the same host.
1: github.com/florianwolters/florianwolters.github.com
CNAME file content: blog.florianwolters.de
DNS CNAME: blog > florianwolters.github.com
2: github.com/florianwolters/pear/tree/gh-pages
CNAME file content: pear.florianwolters.de
DNS CNAME: pear > florianwolters.github.com