Thanks to some remarks from @etienne in regard to overriding the freedombox config files (Reference Post) the issue seems to be solved with the following steps:
Introduce your new domain under Plinth > Configure > Domain Name (i.e. custom.com) This will trigger LetsEncrypt to obtain a certificate for your new domain Once you get the certificate, you may revert back to your initial domain to access FBX.
Follow steps in this guide to create the folder structure for your new website.
When creating your conf file, name it with a prefix of 01-(i.e. 01-custom.com.conf).
The contents of your 01-custom.com.conf should be in line with the below: