Its closer to a config file / internal functions that modify the state variables of a system instead of generating objects. The junk DNA doesn't explicitly get read, but it interacts in nonlinear ways with the executable "text" portion of the DNA.

Also disclaimer: My only knowledge of this is from Nessa Carey's The Epigenetics Revolution and some additional online reading.

Or, more like Makefiles, and an enormous amount of cache for the runtime and build system, but this cache never really gets invalidated.

Basically it's like using a "buggy filesystem" (like ext2) that only shows the first ~16000 files in a directory. So having too much junk can hide stuff, having too little of it can uncover files that evolution carefully hid, and so on.

No, this is the wrong metaphor. You want the right metaphor: one brilliant coder, 10 total newbie coders, and five cats walking all over the key boards. And no delete function at all!

depends on what you consider non-coding, too. the ribosome is mostly made of RNA, but it's not turned into a protein. if your ribosome breaks you can't make proteins.

Imagine copying and pasting random junks of code from around stack overflow into your script and commenting it all out, thats kinda a better analogy. 20 lines there, 400 lines in reverse over there. Sometimes they get uncommented in cancers.