Actually, it might. Per section 1:
> The "Corresponding Source" for a work in object code form means all the source code needed to generate, install, and (for an executable work) run the object code and to modify the work, including scripts to control those activities.
Mastodon is written in Ruby, and large Ruby programs (particularly Rails) usually use Ruby DSLs for configuration. It's very plausible that changes to the config would trigger the AGPL.
But let's be clear: copyright holders get to decide when they enforce their copyrights. They aren't beholden to enforcement the way that trademark holders are. It's perfectly reasonable and legally consistent for a copyright holder to prioritize egregious violations (like TRUTH's) while ignoring smaller ones (like Joe Schmoe forgetting to publish his tuning changes).
Portions modified may not be subject to any form of copyright protection if the original code and/or modifications are purely functional. Purely functional expressions that lack any creative element are not copyrightable to begin with.
This is a more abstract observation than is perhaps relevant to the situation at hand, which involves a group of people modifying software components that the current body of software copyright law would not consider "purely functional."
Let me ask another way. Did these modifications require a recompile? Pulling a word out of a config file would not constitute a “modification to the software”, merely use as intended.