There are valid reasons for the question. For example, if you wanted your users logon script to always reflect any changes you made at a central file store on your Domain server, the logical place would be to precede the logon script with either an additional script in the Startup or perhaps the Shudown optional scripting locations.
Now my concern -- you do not have the security tokens during a Startup or Shutdown procedure to access your Domain server.
Second issue. If this is a Domain, enabling logon scripts is a Group Policy object that could easily be set for all users. If a Workgroup, the process is decidedly more complicated.
In general, the solution would be to have a generic logon scripting:
. layer one -- identical logon scripts, that essentially call:
. layer two -- a script to copy over the existing %userprofile% logon script; and then would call:
. layer three -- what will be the finally executed logon script. Because scripting wait states and recursion are a little tedious in WSH scripting, I would use .CMD files with the START /xxxx paramter settings to handle all three layers.