When you make changes with msconfig, it specifies how your computer will behave the next time you start it up. Enditall kills things right now, rather than having to wait. The other advantage of enditall is that it doesn't change your computer configuration, so that the next time you boot you will have all the stuff you had before. With msconfig you'd have to remember what you turned off so that you can manually turn it back on again.
And, one other thing to consider: msconfig only shows you the processes and software that *want* to be seen. Lots of other stuff will hide in the background and won't be listed there, so you can't turn it off with msconfig. Enditall usually zaps those things too.
I just have to say once again, though, that, ultimately, I was surprised how little I really needed to turn off to get OS stripped down for capture.
I experimented several times -- sometimes finding that I'd shut down things that I needed or that locked up my system -- and, in the end, I ended up killing off my virus protection and a companion program for my graphics card and that's about it.
I still have about 26 processes running (according the my Task Manager) when I do a capture, but I don't think any of them are optional, and none seem to cause any problems.