It doesn't, because "the Unix philosophy", in the meaning implied by your question, is oversimplified nonsense. There is both utility and architectural value to be found in integrated user experiences. To throw out just a few small examples, such experiences done well may reduce context switching and/or build on the user's deep skills in the integrated environment (esp. w/ Emacs' and vim's text manipulation support). Likewise, there is immense utility in a scriptable, user-programmable working environment, especially for developer's tools.
Also note that Emacs and vim often comply with the oft-cited first bullet point (there's more than one!) of "the Unix philosophy" by reusing powerful yet single-purpose external tools under the hood. Case in point: git(this thread!), ag/ack, and so forth.
So please forget the idea that bullet-point-one of the Unix philosophy is a sacred tablet from some ridiculous Unixy religion. It's just an old, occasionally useful, architectural rule of thumb that applies in relatively narrow circumstances relative to the breadth of modern computing experiences and implementations.
Haha, sorry, I know my question was begging for that response. But even if you (and many others) appreciate tighter integration, others would appreciate the flexibility of being able to pick and choose what they like from emacs without being overwhelmed by what is an incredibly foreign environment.
You can use emacs to run elisp the exact same way you'd use a python script, emacs is pretty much an elisp shell. And there is no loss of flexibility, emacs doesn't reimplement everything from the ground up and most features are reliant on "shell programs". Dired for example is pretty much a sophisticated skin over an ls call if i'm not mistaken.
Also note that Emacs and vim often comply with the oft-cited first bullet point (there's more than one!) of "the Unix philosophy" by reusing powerful yet single-purpose external tools under the hood. Case in point: git(this thread!), ag/ack, and so forth.
So please forget the idea that bullet-point-one of the Unix philosophy is a sacred tablet from some ridiculous Unixy religion. It's just an old, occasionally useful, architectural rule of thumb that applies in relatively narrow circumstances relative to the breadth of modern computing experiences and implementations.