For security reasons, the Bitnami Prestashop Image is set up with those strong permissions that can be restrictive for some users. If you're using your "own custom user" to access via FTP and you want to be able to modify all the files with that file, I recommend you to connect via SSH to your server and give write permissions to that user. For example, if you're using the user "CUSTOM". You can execute:
sudo chown -R CUSTOM:daemon /opt/bitnami/apps/prestashop/htdocs/
After that, you shouldn't find permission issues.