Udacity's CS253 "Web Development"[0] taught by Steve Huffman does exactly that. It uses Python on Google App Engine and Jinja for templating.
It starts from the basics. Tackles forms, handling requests and parameters. Cookie handling and authentication. Hashing (on which he even shares a bit of Reddit history: they didn't hash passwords which allowed them to detect spam accounts using the same password, but then Murphy's Law hit and the laptop was stolen and the database with it). Indices, joins, etc..
He discusses Reddit's architecture evolution and why they made the choices they've made given the context, etc. Sometimes, it boils down to "we chose it because that's what we knew". Other times, "we chose it because we hated the other thing". It's fun to hear him talk about this.
The course is pretty cool and the subtitle "How to Build a Blog" is an understatement. There was no stress on writing beautiful code or something, but the message is clear.
Another course I'm looking into is Stanford's Startup Engineering CS184 by Balaji S. Srinivasan and Vijay S. Pande. It has been discontinued. I just did a flyby and it's pretty much what you're talking about (they do both "big picture" with their reading list (Thiel, Graham, Andreessen, etc) but don't shy away from getting down to "viewport" and CSS, setting up stuff on Heroku, talking about tmux. They apparently did a lot of "why" stuff).
In my opinion, much of learning is done as it would be in a physical system with non catastrophic consequences: doing stuff, analyzing phenomena by the changed quantities and state/side effects, deducing the governing laws. You learn much about CSS from inspecting elements and changing stuff then reading MDN, than from the opposite. The first gives you something to anchor new knowledge to as opposed to starting with a setting that is too formal and abstract..
I mean, even doing Physics one can't be so exact not to approximate and neglect the influence of something at some point and just do a basic thought/physical experiment.
[0]: https://www.udacity.com/course/web-development--cs253