The installer uses mkpartfs which recommends use of the file system specific tools for reliability and makes the user explicitly Ignore the warning about misaligned blocks. (Note: from memory) We should take a look at the simple installer script we provide (meta/recipes-core/initrdscripts/files/init-install.sh) and make sure it doesn't make the user choose to ignore scary seeming error messages.
This bug has been fixed by: http://git.yoctoproject.org/cgit/cgit.cgi/poky/commit/?id=577a9145124582de7c4288dffe993eb7a3459162