Please add code samples of your overridden Media Library class, it's hard to know what the issue is when you have custom code involved

Do you really need to add this to the view? Why not add it to a JS file that loads after jquery and target your selector using a css class or data attribute?

Are you using some sort or URL redirect module that allows you to create redirect rules from within Sitecore?

Please add further details to clarify your question. At the moment it is unclear what you are trying to do. What are the user defined settings? Who is the user, the content author or a site user? Which settings are you trying to override?

Thanks, answer added, and updated - BuildUrl() would be probably a better method to override just for the custom link generation part.

Try inheriting from Sitecore.Links.UrlBuilders.ItemUrlBuilder and override the Build(item, options) method. BaseUrlBuilder doesn't appear to be registered in Services Config so this still does not appear to be using the IOC container.

Did you disable EXM as well by setting exmEnabled:define=no in the web.config?

Try moving the config to a zzz.Last folder and check if the patching order is correct. It will let you know if it's an issue with the config or load order.