For Azure integration you can just send the necessary values to Acumatica(or your partner) and they can update the Web.config(as Dimitrii said). And I wouldn’t recommend using a customization plugin unless you really know what you are doing, particularly on a SaaS instance. Errors with the config file will prevent your instance from starting.
In regards to the code snippet webconfig is never defined. Looking at the git history that seems to just be a typo, “webconfig” should be “file”. He changed it from modifying web.config to modifying packages.config but did not update the variable.
Original Code
String webconfig = File.ReadAllText(Path.Combine(PX.Data.Update.PXInstanceHelper.RootFolder, "web.config"));
webconfig = webconfig.Replace("<add key=\"ReminderVisible\" value=\"false\" />", "<add key=\"ReminderVisible\" value=\"true\" />");
File.WriteAllText(Path.Combine(PX.Data.Update.PXInstanceHelper.RootFolder, "web.config"), webconfig);
Updated Code
String file = File.ReadAllText(Path.Combine(PX.Data.Update.PXInstanceHelper.RootFolder, "packages.config"));
file = webconfig.Replace("</packages>",
"<package id=/"Newtonsoft.Json/" version=/"6.0.8/" targetFramework=/"net451/" /></packages>");
File.WriteAllText(Path.Combine(PX.Data.Update.PXInstanceHelper.RootFolder, "packages.config"), file);