Kloxo-MR 6.5.0 not design to handle letsencrypt.
If you want domain-based SSL, you need using Kloxo-MR 7.0 under CentOS 6. That it.
Sorry to ask you,
but is it good practice to use latest KloxoMR7 beta as daily server with 50 domains and cca 10-20 customers?
Currently I'm using old original Kloxo, and I think to migrate to CentOS 6.8 and Kloxo 6.5.0.f, actually server is already configured and working with 2 domains.
My idea is maybe to wait one more year, when is Kloxo MR7 out of beta, and then to migrate everything and use https.
Just your opinion please, thank you.