There are arguments either way with the user-startup.
The original idea with it was that the startup-sequence, which contained the important system booting stuff, was meant to be left alone. Any additional assigns or programs run on startup could be added to the user-startup.
If some kind of problem developed, you could disable the entire user-startup, thus narrowing the problem down to the startup-sequence or the user-startup.
I kind of use it in this fashion, but of course we all add extra stuff that has to be run early in the main startup-sequence.
A disadvantage is that it's harder to see what's going on during startup, as first you have the startup-sequence, then the user-startup, then the contents of the WBstartup drawer.
The bottom line is that the OS is flexible enough so that you can use user-startup/WBstartup if you want to, but if you don't like/need it, then don't use it.
Personally I use all 3, but I know it could be tidier, and slightly faster if I just use 1 startup-sequence.
Anhony.