How to help students comprehend the HTML document flow?
Absolute positioning as bad practice

Referencing the StackOverflow question, "Is it considered bad practice to use absolute positioning?", the consensus is, just like nearly everything in CSS, "it depends".

But let's just throw some data at the topic:


More than 50% of website traffic is presumed to be from a mobile
device. Using absolute positioning (especially when positioning from
body) will impact how mobile viewers see your content. 
There are
literally thousands of possible combinations for screen sizes and
resolutions. Positioing absolutely will break on most viewports.


These are the two biggest reasons to rely on document flow as opposed to positioning the elements yourself. But obviously, the student(s) are trying to solve a problem they have with the hammer they have.

So, maybe instead of trying to convince them not to, show them how bad it performs under real world situations and provide some alternatives.

Define the problem


Open a browser like Chrome, and using the bottom left corner of the browser window, resize the window. Elements positioned to flow around constraints will reposition, absolute elements will not.
Also in Chrome, open the developer tools and open the "device tool bar". This will allow you to look at the page in a simulated screen resolution for a number of devices.
Visit the web page on the student's phone. Switch the phone between horizontal and vertical views.


Better Practice


Use a grid. There a number of grids available like those that come standard with Bootstrap, but sites like css-tricks.com also have a number of smaller implementations that actually describe the basics of a grid, like this nice one from Chris Coyer.
Be right on the cutting edge and teach grid layout directives that are only in draft proposal (but work in some canary browser releases) this other tutorial on the Mozilla Dev Network.
Be less on the cutting edge and teach Flex.
Introduce viewports to trigger css changes at certain screen size


After some or all of these, reflect by going through browser resizing, etc. explained above.

Some other talking points

I'm not sure what kind of project the student is creating, but some other things to consider under certain circumstances:


Their experience with x, y coordinates will help them a lot if they are doing game development or graphics within a canvas tag or creating SVGs. Discuss when those are appropriate to use in HTML (SVG icons for links under certain viewports, eg).
Discuss content visibility and re-flow on devices of different resolution. Moving or hiding information based on user context (are they on 
a desktop with lots of viewable space and a mouse, or are they on an iphone 4 and just want to click the 'buy' button?).