I've just tried deploying an ASP.NET Web Forms application to an xsp4 server (I've made sure it's linked to .NET 4.5 in /usr/bin/xsp4). Removing the tags that are from bundles and as such don't have a specific path (such as <asp:ScriptReference Name="MsAjaxBundle" />).
If I remove/comment out these from my Site.Master, it successfully runs and XSP doesn't throw an error. However, that removes the scripts that these bundles provide, such as MsAjax, jQuery, Bootstrap, and WebForms.
The specific error generated by mono is Assembly 'System.Web.Extensions, Version=4.0.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35' does not contain a Web resource with name 'MsAjaxBundle'. (If I comment out the MsAjax line in Site.Master, the reference to jQuery, which is on the next line, replaces MsAjax in the error).
EDIT: Just tested this, appears to happen with mod-mono as well.
EDIT, again: Yes, I'm very much aware that .NET Core is the new way of doing things. My new applications, including V2 of this one, is written with .NET Core. This is a legacy application.