I'm sure refilling magma can appear 2 or more levels above the current level of the pool. So if you drain it to 5, new magma can appear from 6 to maybe 8. However, magma filling from the bottom is still true in a way. New magma never appears above floors.
I've drained a magma pipe and then stared at it for a while and never saw anything like that happen.
One thing I did notice is that if, say, level 5 is full of 4/7 and 5/7 magma, it will still spawn full 7/7 blobs on level 6, which then fall down into the available space on level 5.
Is it possible that in whatever instances you observed, the pipe happened to generate magma on the same tile two times in rapid succession, so that there was still a bit of magma on level 6 allowing the new magma to appear on level 7?
I can imagine an experiment to test this.
I've confirmed that magma creation pathing will go up through grates or horizontal bars.
Build pumps to keep a magma pipe drained down to a given level, which we'll call level 5 because we've been using that example so far. On level 7, built alternating rows of floors and grates over the magma pipe. Then fill the level with cats. If the cats die, magma must be appearing on or above level 7. If the fort runs for a long time without burning any cats, then magma appearing two or more levels above the current magma level in the pipe is an uncommon event at best.