This is a "it depends" answer.
First, the default IE template in UEM does not save plugins itself, which you already found out. It does however save the settings that specify which plugins are enabled/disabled (HKCU\Software\Microsoft\Windows\CurrentVersion\Ext\Settings).
Second, it depends where the plugin is installed. Is this a plugin that installs in the user profile? If this is the case, you should really check up front if you want to save that plugin using UEM. If the plugin takes much space, you must ask your self if you want to save it using UEM, because it may impact user logon/logoff duration. If you choose to save the plugin using UEM, create a new Config File (INI) and specify the file/registry locations that need to be saved. You can use the UEM Application Profiler, Procmon or Regshot for that.
If the plugin is installed on computer level, make it part of the base image and use the registry or ADMX templates for enabling/disabling the plugin for specific users using conditions or condition sets. You can use the resources below for that. You can use ADMX-based Settings or Registry Settings from the User Environment tab in the UEM Management Console.
Disable Particular IE add-on via registry – Siva Mulpuru's Blog --> can also be used for enabling
Does this answer your question?
Great answer! Thanks.