Here’s a precedent: a MIDI file doesn’t break copyright just because it could be used with a soundfont you don’t have rights to, to generate an audio file you don’t have rights to (because it’s a derivative work of the soundfont).

Or, even simpler, a text file doesn’t break copyright just because you could print it using a copyrighted font you don’t have rights to.

A game-modding program is exactly the same thing, here, as a MIDI sequencer or a printer; and the mod itself is exactly the same thing as the MIDI file or the text file.

In both cases, you’ve got 1. a high-level description of a thing you’d like to make, and 2. a program that renders that high-level description using a supplied asset library. Presumably, there’s nothing stopping you from using an entirely public-domain asset library. Some unscrupulous people just happen to want to use a copyrighted one. (Just like some unscrupulous people happen to feed BitTorrent clients torrents that point to copyrighted material!)

In both cases, there’s nothing inherent in the software that leads to it being used in that manner. It’s the user’s choice to point the software at an asset library—or a torrent—which contains content they don’t own.

Of course, by this line of argument, a page with instructions for how to use the software in combination with the game’s copyrighted asset library, would be breaking copyright in about the same way The Pirate Bay is. The site hosting the software itself would best refrain from doing such. (And better yet if it comes with such an open asset library, such that it can’t be argued that breaking copyright is its only purpose in practice.)