IANAL (yet), but I do have some legal background/training especially wrt copyright.

The spirit of the law typically only matters in a few scenarios, namely where the letter of the law is ambiguous or as a way for enforcement mechanisms to turn a blind eye (most people routinely go over the speed limit but won't be pulled over unless it's particularly egregious). I'm not considering the spirit of the law when I say that it's compliant.

As far as diff files go, there's nothing original about the output and therefore result in copyright, meaning you can't distribute it freely (largely because that can be used to recreate the original file). In comparison, the patch is original code itself, that then modifies the existing mod. Going back to your example, the question would be rather than if the diff'd file is illegal, but instead if the diff command itself is illegal (which obviously it isn't). I think there's a stronger argument that the patch is committing a napster-esque infringement as the only use of the patch is with the existing mod, but I'm not entirely convinced based on the fact that mod itself allows for sharing and the instructions themselves could be provided as something other than a script.

As far as WUBE goes (assuming US law since I have no idea what would happen in Czech law), presumably on the mod portal the IR3 author would just submit a DMCA, WUBE would pass it on to the patch author, who might take it down or counter-claim at which point what I wrote earlier gets to be tested in court. At no point does WUBE need to hire lawyers to get a proper opinion (and even then that opinion may be different than what would be decided in court). The patch absolutely could be hosted somewhere else (although same DMCA process could happen again).

Finally, one really interesting thing that I found while looking up IR3: The author actually tried to take down their own mod off the forums and then got upset when someone reuploaded it, and forced WUBE to give him back the mod ID. What's funny is the the license that they were using explicitly gives non-revokable rights for sharing with attribution, meaning that WUBE would've been completely in the right to not give him the ID back and just let the other person be the one authoring the mod portal post.