I finally got it to work. The issue was permissions The problem was that I was working on the permissions of /etc/letsencrypt/live and missing the fact that it was just a link from /etc/letsencrypt/archive. If I had to change permission, it should be there at the archive directory.
After changing the permission of /etc/letsencrypt/archive to 0755, I was already getting Syntax OK from apachectl configtest and openssl was already able to read the file.
I hope this post gets to the dev. team. Is this normal behavior? The steps I took to setup letsencrypt is mentioned in the original post including how I got the certificates, which was done Auto. I believe that something done in Auto should work fine. I don’t know if my user credentials had something to do with the permission issue. I installed letsencrypt using a non-root User and I did sudo.
I also got this running at Server Fault. Also marked as answered there.
More power to Let’s Encrypt!