After reading https://shopify.dev/tutorials/modify-the-online-store-channel, I see there are several ways to modify a shopify theme with an app. But whats the preferred way to do it in 2020 ?
Some details: I want to modify the cart page to add a progress bar, based on data stored in my app database.
Unfortunately, there are no cleanup hooks, and that was the reason for Shopify to start working on App Sections. If you have concerns re left overs, you can go ahead with ScriptTags. ScriptTags are removed from the store once the app is uninstalled, leaving no traces.