Yes, we mentioned that the Bitnami solutions doesn't use the .htaccess files by default. If you were using a shared hosting in the past, you only had the .htaccess files to make changes in the Apache's configuration but you have control over Apache so you can do whatever you want in the instance.
The httpd.conf file is the main configuration file of Apache and then we include the bitnami.conf file and the different configuration files of the applications. As you want to enable a module in the Apache's configuration, just enable it in the httpd.conf file but in case you want to make a specific change for your application, please use the configuration files under apps/your_app/conf.
I hope this guide helps