Despite what I'd like to believe (and maybe even what I'd like you to believe), making something in C++ doesn't mean it can't have its resources modified or even stolen. ENIGMA (being C++) makes sure that code isn't such a resource. No one can decompile your game. However, we do have a problem.
Because ENIGMA will be a regular system, unoptimized output executables will have the same basic format. Furthermore, because it is open source, an encryption algorithm is even more futile than it was in Game Maker. I can't just hide a seed and expect everyone to give up before finding it.
Now, in R3, rooms were stored as an array in the source code. This means that it would take a good amount of skill to modify them, but it's still feasible. Someone with a decent knowledge of how GCC handles such could probably make a tool to do it. If ENIGMA were to inherit GM's better disassemblers, we could possibly face problems with such (the hope is that since no one can get all of it, no one will write a tool to get some of it).
Fortunately, as long as you let GCC optimize your code, it should be too irregular to be removable by an automated tool. (Even if it was removed, it couldn't be decompiled other than manually, don't worry.) However, I'm not sure about unoptimized code. It would be far too much work to decompile it back to EDL (especially with the C++ goodness that gets thrown in), but it may be possible to remove entire events and replace them (making games easy to mod or cheat).
What's more, unified sprite and sound encryption is worthless. Pidgin doesn't encrypt passwords it stores for users because the developers understand that in an open source project--and for that matter, in any other project--doing so accomplishes nothing. So ENIGMA can not have a unified encryption system to protect non-code resources.
Personally I don't see this as a problem. However, I know one of the reasons people are in awe of the idea of C++ is that they think it will protect such resources. I can't think of a decent game whose resources aren't an open book (there are many Windows resource extractors. Not to mention, you Valve fans, think Garry's Mod). But, I can think of a way to fix this.
R4, as some of you are aware, will allow you to define C++ functions for use in your game. This is a great way to do with DLLs (but do note that external_define has been done for months). I could allow the implementation of a function called resource_encrypt (and one called resource_decrypt) to allow users to define their own algorithms. This would be done with the hopes that such an algorithm would not be in a uniform position in the executable every time.
If it was, it'd be as simple as writing a tool to look for like bits of code and extract the new stuff. Though they could still not decompile your code (and I am talking about the algorithm), they could call the decryption algorithm themselves, right where it sits, on whatever resources they extracted. Frankly, I think our better bet is to not waste time on encryption.
To protect room tampering, ENIGMA could hard code their creations in a large function (which would be optimized hopefully to un-uniform gobbledy... but it could still be replaced by a determined expert).
The function could be implemented conditionally; only executing if it has been defined by the user. This is just an idea I'm putting out, thoughts welcome. Especially from assembly people.
TL;DR: Paranoia resulting from the idea of really talented people wasting their time hacking games. Mods are inevitable, resource extraction is hard to stop, decompilation highly unlikely (as in, no one will waste their time on a huge game, and automation is impossible).