I've never used a magma piston either, so my comments are theoretical...
Constructed walls/floors are destroyed when you cave them in. "Natural" rock/soil fuses onto the surface it lands on (assuming it doesn't smash through a roof) (and soil can transmute into something else in the process, but that's a different issue). Thus, the piston falls and fuses with the floor, you dig it out, cause it to collapse (onto magma), dig it out...
The piston functions because the magma displaced by the falling piston teleports up to the top of the piston, where you're supposed to lead most of the magma off for usage, while obsidianizing a small bit to extend the piston to make up for the part dug away at the bottom.
Also note that you can't do this in the magma sea, because "magma flow" covered by magma annihilates anything falling onto it (except, I think, [un]living creatures), so the whole piston would just disappear the first time you dropped it. You work around that issue by dropping the piston into a room which takes magma from the sea.
I've seen mixed results from trying to cave-in a mixture of "natural" rock and constructions, so I'm unsure how it would work. If your self contained fortress was completely dug (i.e. no constructions), and you'd dropped it onto rock (which can be in the sea) your structure should fuse with the rock. However, I expect any creatures inside that fortress to suffer the effects of being dropped.
* The term "natural" is used to cover player made obsidian.