Permissions: What people are referring to here is that some registry keys are protected by Windows, and require Trusted Installer (TI) permissions to change those keys, as a security measure to help prevent malicious stuff from tweaking parts of the operating system. NTLite automatically handles this for people and there's no reason to use other tools or commands to modify permissions if a user integrated the tweaks using NTLite.
User Account Control (UAC): This is the setting in Windows that causes all those message prompts that appear asking a user if they are sure they want to run a program or do some action. This is another security measure, and the proper way to tweak it isn't through hidden registry keys that many people use, but instead to just move the slider down to "Never notify" which can be done with an integratable registry tweak.
Local_Machine (HKLM): This branch of the registry affects all users on a computer. Not every tweak will work here, as some tweaks only function if placed in the Current_User tree of the registry, and that is by Microsoft's design.
Current_User (HKCU): This branch of the registry only affects the currently logged in user. Not every tweak will work here, as some tweaks only function if placed in the Local_Machine tree of the registry, and that is by Microsoft's design. It should be noted that some tweaks work in both Local_Machine and Current_User, and in those cases the Current_User takes precedence if conflicting values exist.
Group Policy Object (GPO): These tweaks are overrides that do not directly alter Local_Machine or Current_User tweaks, instead if a group policy key is enabled it tells the operating system to ignore the relevant key in those two branches and instead does what the group policy wants. The main point behind group policies is for sysadmin to prevent users from changing settings, which is why the red text appears in places saying, "Some settings are managed by..." The other reason people use these, is because they also prevent Windows from changing settings, so it helps to stop some of the overwrites and overrides previously discussed, which is the lazy way to solve a problem.
Integrated: NTLite can integrate settings directly into an image, meaning they are in effect before, during, and after the installation of Windows.
Post-Setup (Before logon): This has been reworded in NTLite, and it used to say "Machine" in parenthesis. By inserting commands or registry tweaks here, it waits to apply them until Windows is installed and preparing things before the first user logs in.
Post-Setup (After logon): This has been reworded in NTLite, and it used to say "User" in parenthesis. By inserting commands or registry tweaks here, it waits to apply them until Windows is installed, and after Post-Setup (Before logon) is applied, then after the first user logs on it applies these.