I just graduated from CU, and I'd agree. Just based on anecdotal evidence comparing w/ friends from Cal, MIT, Harvard, etc, I think all of these 'top' schools do a pretty good job of mixing theory and practice within the required/core CS classes, and then allow the students to decide for themselves which track they want to follow. For instance at Columbia, we have tracks in AI, Applications, Theory/Security (forget the exact name but this is theory & algorithmic heavy), Systems, etc. These tracks comprise several senior / master / phd level courses which you usually take in your last year or two. No matter which track you go into, all CS majors take the same core CS classes in data structures, basic CS/compiler/language theory, statistics, linear algebra, etc.
I can't say that any of the core classes involve navigating a huge codebase... there are certainly some upper level track classes (especially in Systems) that give you that experience, but I do agree that is relatively uncommon.
Honestly so much of the learning happens in extracurriculars (Hackathons, CS/tech clubs, etc) that it's hard to keep track of which skills you learn in classes vs just doing other activities with friends. I think the power of college resides in the strength of such extracurriculars.
It's sickening to hear that you had to go through such experiences. Funny that the 'default' scanner technology didn't set off any alarms. Many of these policies just seem to provide the sense that we're safer, rather than actually do anything to remove real dangers.