After reading a few support tickets I was able to find a solution to this.

After merging all the PDF's into one document I noticed the auto font was there just not active. To resolve this I opened the merged PDF document and used the recalc appearances function. 

This worked unless you have the Acrobat extension installed. In that case you need to disable open PDFs in Adobe option. 

The end result is the PDF with Auto Size and other functionality display correctly in your browser and when you download to your local computer to open with Adobe Reader, Adobe Acrobat or your favourite PDF viewer. 

Sample Code: 

        Dim filename2 As String = "MergedDocuments.PDF"
        '* Open document And Recalc Appearances
        PDFdocument = providerPDF.Import(File.ReadAllBytes(Server.MapPath("~/") + filename2))
        PDFdocument.AcroForm.ViewersShouldRecalculateWidgetAppearances = True
        If File.Exists(Server.MapPath("~/") + filename2) Then
            File.Delete(Server.MapPath("~/") + filename2)
        End If
        Using output As Stream = File.OpenWrite(Server.MapPath("~/") + filename2) ' Export PDF to the output filepath
            providerPDF.Export(PDFdocument, output)
        End Using

        Dim url As String = "PDFViewer.aspx?Document=" + filename2
        Dim sb As New StringBuilder()
        sb.Append("<script type = 'text/javascript'>")
        sb.Append("window.open('")
        sb.Append(url)
        sb.Append("');")
        sb.Append("</script>")
        ClientScript.RegisterStartupScript(Me.GetType(), "script", sb.ToString())

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