It may be possible that when that much water tries to teleport, it ignores floodgates, but that sounds sketchy.
I think what happened was that it appeared the ocean was draining past the floodgates, but what really happened was 2 unrelated things simultaneously: the aquifer finished filling the chamber on one side of the floodgate, and the ocean water teleported into the empty tunnel instantly. So it looked like it was going past the floodgate, but actually it was just the aquifer filling the void on one side and the ocean filling the void on the other. Once both voids were filled, it took a while but the ocean eventually settled down. It wasn't really going through the floodgate. Perhaps I should change the title of this thread. Unfortunately it doesn't drain (much) with the floodgates open either.
Even breaching the aquifer wasn't a problem; I did that first. I channeled out a large chamber under the aquifer and had my miners standing on floor grates, so that when my miners dug out from the aquifer the water fell through the grates, leaving the miners time to dig a dozen of the aquifer tiles out.
So you 'd'ug those tiles below, then c'h'anneled the tiles above, right? Then built the floor grates as you channeled each tile? Where did the water go when it was falling through the grates? A large basin? I'm just curious, as I have a large aquifer project and this sounds useful.
Well that is one good thing that came out of this - it turned out it's a GREAT way to safely open an aquifer. Note that it won't help you get past an aquifer that you're trying to dig down through; this is for when you are digging at the edge of an aquifer and you for some reason actually want the water to come out and fill the mine. You have to already have a way to get to the Z level below the aquifer to do this anyway.
As for the method in detail, I'm not sure you're misunderstanding my explanation, or I'm misunderstanding your summary, so I'll just explain it from scratch:
Let's call the Z level below ground -1, the one below that -2, etc. On about Z level -4 I found the outer boundary of my aquifer. I dug out the dry stone around it until I'd exposed a whole wall of damp stone. Then I dug a large chamber underneath that wall of damp stone on Z level -5. I dug a 1 tile wide channel right by the wall on Z level -4, and covered the channel with grates, on Z level -4. That way my dwarves could still get to the exposed aquifer wall across the channel. Then I dug out the wall of damp stone all at once. The water that came out ran down through the grates into the chamber on Z level -5, so Z level -4 didn't get too much water until the dwarves had time to get out.
You couldn't really use this as a technique to get below an aquifer because if you could find a dry place on Z level -4 to dig down to Z level -5, then you wouldn't need to breach the aquifer anyway.
Maybe if you used pumps you could pump UP to a chamber on Z level -3, but then the wiki already says you could use pumps to breach an aquifer so that's not really news to anyone.