The whole "old installer" and "bootable disk" has been a pain-point since 10.8 for me. I have done 4 or 5 clean installs for friends in the last 6 months, and I tried to make a 10.10 or 10.11 bootable USB... no go - each time, a new issue.
I have ended up every time using my older 10.8 (ML) install USB every time, then just firing off the free App Store upgrade to 10.11.
In newer Mac's (2012 onward IIRC) you can just boot into a net installer, and it goes and fetches the installer from the internet before re-installing.
I have ended up every time using my older 10.8 (ML) install USB every time, then just firing off the free App Store upgrade to 10.11.