As someone who has created several skunkworks projects at large companies which got shipped, I'm wondering what exactly the OP's definition of "Modern organized software" is. I have definitely worked in an environment where creating a skunkworks project was next to impossible due to a toxic micromanagement culture, but in that case I left the company instead of assuming that it was representative of the software industry as a whole.

EDIT: I'm also confused about the talk of "corporate rebels" on one hand, but the complaints about dealing with processes on the other. What do you think corporate rebellion means? Do you think that "rebellion" means not having to deal with any attempt to stop what you are doing? Frankly, trying to sneak around processes is half the fun!