You are correct. The shells are different. However, for the question you originally posted...
["I want to run a script that just tells the command prompt to execute the dos command "dir" or "cd" etc."]
...the differences should not matter. The shell script I gave contains a series of basic commands that are the same across all Windows platforms.
If you are now asking if it is possible to write a shell script that will work on Win95 and not on WinXP. The answer (obviously) is yes, but the same is also true of vbscript using the WScript.Shell object.
For example, if you want to run a shell command (like "dir" or "cd") using vbscript and WSH you have to call the WScript.Shell object. Calling this object simply creates an instance of the shell that is native to the Windows version you are running.
ex)
'START CODE
CONST SVCNAME = "Schedule"
Set ws = CreateObject("WScript.Shell")
ret0 = ws.Run("net start " & SVCNAME,0,"True")
If ret0 <> 0 Then WScript.Echo "There was a problem starting the service: " & SVCNAME
'END CODE
If you are worried about cross-platform viability, you should use vbscript to do some OS detection to run different subroutines based on the different OSs you are planning on supporting.