It seems that aspnet CDN doesn't serve minified versions of WebForms.js and WebUIValidation.js. So I found a shorter way than the legacy Bundling and Minifying which works for me & thought to share in case any one will find it useful.
The quick solution for me lies in minifying them myself, placing them locally, then calling them as follows:
<asp:ScriptManager runat="server" CompositeScript-ScriptMode="Release" EnableCdn="true" LoadScriptsBeforeUI="false">
<Scripts>
<asp:ScriptReference Name="WebForms.js" Assembly="System.Web" Path="~/Scripts/WebForms/WebForms_4.6.min.js"/>
<asp:ScriptReference Name="WebUIValidation.js" Assembly="System.Web" Path="~/Scripts/WebForms/WebUIValidation_4.6.min.js"/>
</Scripts>
</asp:ScriptManager>
This will replace just these 2 with a minified local version while the other ScriptManager or Ajax scripts will be intact.