It appears that the "IsHFScaleWithDoc" does not apply with the Workbook Save as PDF option. In the below code, I would expect EXAMPLE1.PDF and EXAMPLE2.PDF to have the same size of header text. They clearly do not show as the same in my test.
I am using Aspose Cells DLL verson 7.0.3.
        Dim ExampleDoc = New Aspose.Cells.Workbook()
        Dim ExampleSheet = ExampleDoc.Worksheets(0)
        ExampleSheet.Cells(0, 0).PutValue("A")
        ExampleSheet.Cells(1, 0).PutValue("B")
        ExampleSheet.Cells(2, 0).PutValue("B")
        ExampleSheet.PageSetup.SetHeader(1, "HELLO")
        ExampleSheet.PageSetup.IsHFScaleWithDoc = False
        ExampleSheet.PageSetup.Zoom = 100
        ExampleDoc.Save("C:\TESTFOLDER\EXAMPLE1.PDF", Aspose.Cells.SaveFormat.Pdf)
        ExampleSheet.PageSetup.Zoom = 50
        ExampleDoc.Save("C:\TESTFOLDER\EXAMPLE2.PDF", Aspose.Cells.SaveFormat.Pdf)