Well, my experiments with the magma pipe are as complete as I am able to make them and I think I have some interesting results.
First, I found a narrow "neck" in the magma pipe to build my bauxite bridges over. I hollowed out a big room around it and filled it with bauxite stockpiles while the magma pipe was draining to that level. When it was safe, I dug out the walls of the magma pipe and started building my bridges. Due to having a legendary architect and a few skilled ones, plus a whole host of legendary masons, this plan worked perfectly and the bridges were completed with no casualties, blocking off the magma pipe completely. They were linked to a lever so I could open them later if necessary.
The results were somewhat interesting. As the magma pipe was draining, some lucky pausing allowed me to view a few "magma splashes" spawned by the magma pipe to refill itself. It turns out they only rise a maximum of about 2 or 3 z-levels above the current level of the magma pipe itself. After the pipe drained below that, the splashes started occurring lower and lower as well. Also, they're not just a single block of 7/7 magma, they are in fact a tower (side view):
7
7
7
327423
777777
777777
After I shut off the flood system and allowed the magma pipe to refill (with my bridges in place) the magma pipe did not refill above my bridges at all. In fact, given enough time it eventually filled back up to 7/7 directly underneath my bridges, but would not go above them. Opening the bridges allowed the magma to begin spawning more columns of magma into the upper section of my magma pipe, and then it eventually refilled back up to its original level.
Effectively this does mean that it DOES fill from the bottom, however it does so in an intriguing and non-intuitive way. I love Dwarf Fortress!
Further research might involve figuring out how DF determines what the "top" level of magma is. If I had kept a tank of magma in reserve and dumped it back on top of my bridges to refill part of the upper half, would it have refilled from that point once the bottom part had refilled? Or does it rely on tracing a path straight up from the "magma source" tiles? I suspect the latter.