Hi,
Transparent mode gives you the ability to get your policy setup around your infrastructure without blocking any traffic. There is no additional benefit. It simply does not take action against traffic. The awesome part is that you can create a policy without the fear of taking down your application. This includes being able to enforce any attack signatures, URLs, parameters, cookies, etc. The idea of transparent mode is to get your policy as close as possible to perfect, meaning eliminating false positives and ensuring that you will be blocking legitimate attacks from day one when moved into blocking. When you feel you have a secure policy but are still going to be blocking attacks you can move it into blocking. Be sure to watch the event logs when you do move it into blocking.
As far as the working with blocking mode only, I would definitely have the policy set to manual mode and not automatic mode. Especially when you traffic that is not necessarily trusted. Automatic will make changes based on the suggestions from learning mode. It stacks up requests based on how many times it has seen a particular request. Manual will require a user to press accept suggestion, where as, automatic will automatically accept it for you. You can see how this could be a vulnerability.
In conclusion, use automatic in a trusted environment, in transparent mode to initially build your policy; when you feel you have a solid policy, meaning, not too many false positives or false negatives, move it into blocking and manual mode.
If you have further questions,
Let me know.
Jake