Programming from the Ground Up teaches x86 assembler from first principles. All on a free OS (Linux using asm). There is a free version available online, but if you want to support the author you can buy it from amazon. https://www.amazon.com/Programming-Ground-Up-Jonathan-Bartle...

A few books exist that try to restore some sort of "complete understanding" :

Software programming starting from assembly language under linux : http://www.amazon.com/Programming-Ground-Up-Jonathan-Bartlet...

A study going from chip design to high level programming :

http://www.amazon.com/Elements-Computing-Systems-Building-Pr...

IHMO this "problem" of "incomplete vision" started when device drivers where introduced in general purpose OS. Professionnal application developpers started to target API instead of hardware. A milestone in this trend for me is Windows 3.0 (1990). This also marks the demise of fixed hardware computers that the hobbyist favored so far.

It's in the download area.

http://download.savannah.gnu.org/releases/pgubook/

Or if you prefer the dead tree version:

http://www.amazon.com/Programming-Ground-Up-Jonathan-Bartlet...