These issues are now resolved in the latest RELEASE version of Interworx. One can now select the domain and subdomains they wish to secure.
For anybody else having the same understanding issue as me: You can select multiple subdomains by clicking them in the “Generate all with Let’s Encrypt” dialogue (CTRL-click).
I habe always selected just one domain and thought I was limited to just one by LE, I didn’t know I could select more (even tried with 4 now, works perfectly).
Cheers,
Michael