When you come back from the bathroom, you want to regain access to your own computer. Think about exactly how you do that. Do you press the power button and reboot, and then enter your authentication credentials into a dialog that you know is your login screen, because you know that every step from boot to login, is intended to protect your interests?
You're stuck there anyways because you can never be sure someone didn't reboot the system, run a keylogger designed to act like the lock screen, and then send your password and reboot the machine.
As the guy you're replying to said, "you know that every step from boot to login, is intended to protect your interests." If you're concerned about someone rebooting the system and running some malware, you should make use of the various features designed to mitigate against that. All PCs these days let you password-protect the BIOS settings, so if you've configured it to only boot from the HD, it's not as simple as an attacker putting in a CD or plugging in a USB flash drive with their keylogger. And for even more protection, you can get a computer with more "enterprisey" features, such as a physical case lock and a chassis intrusion detection switch. If the attacker thinks they'll just open the box up and do a quick hard drive swap or something like that, that's not gonna work. And these days, there's also UEFI Secure Boot. Sure, there are ways to attack all of this, but a BIOS password plus case lock is sufficient for the vast majority of people. If you need more than that, you should probably focus on keeping intruders from getting access to your computer in the first place.
Whether it's user mode per se or not, there are tools to change the behavior of ctrl-alt-delete.
As far as I can tell, that's just a utility that changes the options that are already available in Windows--they're normally controlled via Group Policy. It's not actually running any new code, it's just changing behavior in a way that MS has already allowed. It actually is possible to write your own code that runs when the user presses Ctrl+Alt+Del though; it's called a custom GINA DLL. Of course, if an intruder already has Admin access to install their GINA DLL, it's already too late... The point of Ctrl+Alt+Del is to thwart malware running as an unprivileged user.
PS - The other major thing is that Ctrl-Alt-Delete was originally a DOS-ism that had more to do with dealing with misbehaving, yet not malicious, programs and trying to regain some level of control.
That key combo was selected because no application uses it. Other than that, there's no relation to its use in DOS. Bill Gates has said that he (or Microsoft in general) had wanted a dedicated key for it, but IBM (which was a major keyboard manufacturer at the time) didn't want to add a key for MS. I guess MS eventually had enough clout to get everyone to add the Windows and Context Menu keys, but it wasn't worth changing Ctrl+Alt+Del to use the new keys.