Just had to do some tracking down in order to get this to work, and figured I'd share with the community. The bitnami owncloud package doesn't seem like its under active development, but this would make an awesome bnconfig option to script, hint hint. Anyways....
If you are trying to follow the OwnCloud.org guide to enabling index.php-less URLs then the first step there is to enable AllowOverride All.
Perhaps this is obvious to others, but I changed this setting in /opt/bitnami/apache2/conf/httpd.conf and didn't see any difference... After much head scratching and tracing through bitnami's chain of includes, I realized that this setting needs to be changed in /opt/bitnami/apps/owncloud/conf/httpd-app.conf
Not rocket science, but throwing this info out there in the hopes it helps a future googler. And maybe bitnami will consider adding a short walkthrough of this process under https://docs.bitnami.com/aws/apps/owncloud/administration/ which hand-hold's people through changing this very common configuration setting.