I don't think that you understood my question properly.
My MAIN POINT is that I:
1) First install LAMP
2) Install certificates
3) Install (4) WP modules (with change of /opt/bitnami/apps/mydomain/conf/httpd-vhosts.conf to point me to new generated cert files).
In other words, I cannot see how Apache will be overwriten when I will only after bncert-tool command going to run Apache configuration (per module). Maybe I missed something.
So, my concern was about auto renewal, as I already tried to install it by twice executing bncert-tool command and it works just great. I have two sets of certificates in folder (as I expected).
I only don't know what will happening after 90 days (or less, depends on how Bitnami configured Cron jobs).
A) Did your script will modify Apache in auto renewal?
B) Did your script will modify BOTH SETS of certificates (like first time), or only one? - that was my initial dilema