The position(x-coordinate and y-coordinate) seems like become different,
when use CreateUnoDialog() or use awt's Toolkit's createWindow(),
their Possize(x/y coordinate) are point to different value.

The sample show as following:

REM ***** Sample code *****
Sub Test()
  Dim oDlg1, oDlg2 As Object
  
  oDlg1 = CreateUnoDialog( DialogLibraries.Standard.Dialog1 )
  oDlg1.setPosSize(0, 0, 100, 100, com.sun.star.awt.PosSize.POSSIZE)
  oDlg2 = CreateTopWindow()
  oDlg2.Visible = true
  oDlg2.setPosSize(0, 0, 100, 100, com.sun.star.awt.PosSize.POSSIZE)
  oDlg1.execute()
  oDlg2.Visible = false
End Sub

Function CreateTopWindow()
  Dim oAwtToolkit, oWindowDesc As Object

  oAwtToolkit = CreateUnoService("com.sun.star.awt.Toolkit")  
  oWindowDesc = CreateUnoStruct( "com.sun.star.awt.WindowDescriptor" )
  
  With oWindowDesc
    .Type = com.sun.star.awt.WindowClass.TOP
    .WindowServiceName = ""
    .Parent = oAwtToolkit.getDesktopWindow()
    .ParentIndex = -1
    .WindowAttributes = 0
    .WindowAttributes = .WindowAttributes + com.sun.star.awt.WindowAttribute.BORDER
   End With
   
  CreateTopWindow() = oAwtToolkit.createWindow( oWindowDesc )
End Function
REM ***** End *****

Just Open any Openoffice.org app in normal window(not Maximun) and run the
sample code

When run this sample, it will show two window,
one is oDlg1 ( CreateUnoDialog),
the other is oDlg2 (CreateTopWindow)

The Position of oDlg1 and oDlg2 are same after run .setPosSize():
oDlg1.setPosSize(0, 0, 100, 100, com.sun.star.awt.PosSize.POSSIZE)
oDlg2.setPosSize(0, 0, 100, 100, com.sun.star.awt.PosSize.POSSIZE)

So oDlg1 and oDlg2 will be show on the same position,
but the result is not!