Yes, in the sense that the resources folder is totally un-encrypted and you can replace files with whatever you want. You can also edit scripts to make new types of trees and flowers and such, but a lot of stuff is much more fixed (e.g. animals only have a few parameters exposed).
I'm now rather tempted to expand this a little, at least where it's easy to do so. At one point I was thinking about making a scripting system for plugging animal behaviours together but lots of this generalisation stuff got swept aside because of just wanting to finish the thing!
(On a related note, I would also consider open-sourcing Proteus at some point, but I don't really know how to do this "properly")
(Also I wish I could find the forum post where Ian gave me a crash course in colour-choosing that was a big part of Proteus's look, but I think it must have been on the old The Games Collective.)