Ironclad still owns the original copyright, and you recognized that, which means that their copyright release applies just as readily to anything falling under that copyright.You can't use something in the public domain, tweak it, and then sell it for money. Why do you think the GNU Public License still exists? Because derivative works *MUST* fall under that very same license.
I'm of course assuming the mod is using its own original or appropriately licensed textures and sounds, and doesn't redistribute ironclad or other people's stuff without permission. Otherwise there's of course no way the mod can relicense, own, or even use/redistribute these parts, since all of that requires a license or copyright ownership. On a glance, however seems to me that this is the case; the Ironclad owned textures need to be copied over from the sins directory and all that. Note it also doesn't include a copy of SoaSE.
Anyhow, Ironclad owns the copyright to the game, not the file system its run on, or the mods that run under it. It also doesn't own your word documents if you happen to mistakenly place these in the Ironclad folder. Even if the game displays them in game for whatever reason. A mod that's located in a different directory but run by a game is NOT automatically a derivative work. Even configuration files as such are not copyright protected - they were meant for user modification and thus can be freely modified in whatever way (patents may still apply in certain countries, though, and in some -rather few- countries its also possible to restrict such config file usage through contracts like licenses or EULA).
Likewise, the GPL basically states that you can only use a piece of software with another piece of software if said software is also free.
That's not a given fact for all software or relates to "public domain" software in any way, actually quite the opposite! Its a condition in the GPL license agreement which must necessarily be met for someone to use the software. As in: It is something specific to the GPL and similar licenses, not applicable in general.
If 'derivative work' were as liquid as you seem to think, there'd be little claim for mods being shut down by Fox for being 'based on' the Aliens universe, or a Star Trek mod being C&D'd, as you could claim Derivative, or at best, Fair Use, neither of which has been successfully fought under.
No. I don't think its a derivative work to start with. Maybe you can show files where this isn't the case? I don't claim to have done anything in the ways of a review, I just saw what I saw when installing / playing.