Concerning Linux boot security?

I saw a definition concerning linux boot access:"Boot access is root access". This makes the fact that if someone has physical access to the linux server, he can get root access and copy protected files.

Moreover, if a linux application server has to be packaged and installed "Physically" in companies this will give them access to the files and they can copy them illegally.

I heard of LIDS (Linux Intrusion Detection System) but I couldn’t understand the boot access security.
My question:
Is there a boot level security that enables the fact of packaging server applications and install them in companies without the risk of the code being stolen (especially if it’s in a scripting language php, asp)

Im trying to find different port numbers for Linux server applications such as ftp, web and printing etc…but do they use the exact same port numbers than Windows IIS?