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My understanding -- IANAL -- of the central thrust of the AGPL is that if there is software that runs somewhere else and serves the result to a user, then that is considered a "distribution" of the software and thus requires the source to be made available to said users, if they want a copy. If you run an unmodified copy of that software, you satisfy your obligation simply by linking to where the unmodified source can be found.
So for your title question, I don't think the dividing line is whether your software is directly/indirectly interacting with existing AGPL software, but rather the question is whether your software affects the service provided to the user.
Starting with your first scenario, I presume that you mean a server-side NodeJS script, and that would modify the results returned to the user. Thus, I would think this is indeed a distribution and the AGPL's provisions would require your NodeJS script being made available to the user.
For your second scenario, I'm not entirely sure if you mean a server-side or client-side theme or overlay. If you modify a CSS file that is served to the user, I would think that's a distribution. But if you're writing a browser extension that overrides the default CSS file from the server, then no distribution of the server software has been made, I think. If you edit a JavaScript file that is part of the Mastodon package, I suspect that is a distribution, because that file is loaded to the user in order to use the service. But I'm not entirely certain on this.
In the third scenario, a scraper would be consuming the result returned by an unmodified AGPL software package, so there is no obligation to offer the source code for your scraper.
The fourth scenario is also a "use" of unmodified AGPL software, and so you have no obligation to offer your custom script to your users.