can they own animations...
Yes, although if someone makes something very similar using similar processes and ends up with a similar result, then no.
No, the camo patterns are out there in the world, and any possible rights holders are not around to claim them. In-game textures that use historical camoflage, of course, are a different story.
...or the concept of armor penetration?
Certainly not. They can own their own scripts that dictate how armour penetration is implemented, but not the overall concept. Someone else can come up with different coding and concepts that yield nearly identical results, and the dev team of Iron Front will have no cause for legal action, so long as their own code was not jacked.
If Iron Front brings armor penetration to the table for the first time, can other modders then not duplicate it for free?
Yes! Provided, of course, that they do their own coding, as previously mentioned.
Is there anything that a Paying mod could take away from ARMA2 because they own some part of their work? With how open Arma is, how much could be reverse engineered into a mod, and would the Dev have any legal recourse? Its not about freeness to me, I'm curious as if something that so far has been skipping through daisy fields could suddenly have a toll booth and barbed wire. So interesting that I"m going to have to research it. I'm pretty sure the boundry happens at the money line.
Basically, code, art assets, stuff of that sort, are protected, and this is how it should be. That does not mean that no one else could possibly make a mod based on Operation Bagration in 1944, or even simply a mod of a T-34 or German infantryman. They would just have to use their own assets. As it stands, when it comes to the Russian Front, there does not seem to be much going on, so far as I can make out.
Whether or not any mods can be added to Iron Front is currently unknown. This will be something that would be determined by their licensing agreement with BIS.
Anyway, I am not too sure why there seems to be any consternation over any of this. Of course, free mods will continue to exist for ArmA2. Iron Front in no way infringes upon that. At the same time, the Real Virtuality engine belongs to BIS, and the decision to license it is theirs alone, and they are within their rights to do so. It is up to the dev team for Iron Front to create a sim that we will want to play, and if anybody does not like it, they can wait until a free Russian Front mod comes along.
I might add that they will likely be waiting quite a long time.