Server :: Secure - Filesystem And Partitions To Be Encrypted But Without The Need To Insert Some Code When Rebooting

I have implemented a web application on Linux that I want to deploy and sell to customers. I want to sell ready systems including the hardware. The application is written in PHP/MySQL. What I am searching to achieve is :

1) Find a way so that filesystem and partitions to be encrypted but without the need to insert some code when rebooting. So that if someone gets out the hard disks and attach to another system, cannot have any access to my files or settings. And of course when rebooting (e.g. after a power failure) encryption to be applied automatically.

2) I know that there are ways to bypass root password on a Linux system. Can all these ways be unassigned ? I want the only way to have access to system, to be by using the root password and nothing else.

I have thought of using a virtual server instead of a physical one (like deploying a virtualbox server) but still would like this to be the most secure possible including not only remote but also local access to system.