First off, Sentora (or it's modules) are not built to use varnish. This would be a custom install as yours is and this can break the way different modules work like in your case. For those using a 'default' installation, the certificate manager works just fine with custom entries. I am not sure what varnish requires, but you could try and customize the module to work in your setup or maybe Diablo925 can help you sort it out
