I cannot reproduce this issue.
Please have a look on the demo script for the TLS Tool: https://gist.github.com/floragunncom/11afce28a77219db92f2d76bb5a0b803#file-tls_tool_demo-sh
I used your basic setup to create this script. It generates certificates and later starts up two elasticsearch nodes with those certificates. Works well for me.
Just download the .sh file, make it executeable and run it in a folder where you have write permissions.