If I understand correctly, once you have removed the toilet, you can see that the sewer pipe below the toilet - the black 3-inch pipe that drops down below the floor - is poking up above the floor? And maybe the flange is risen up with it?
Is there anything in this thread that helps?
https://www.trailmanorowners.com/for...ead.php?t=5889
In particular, one of the final pictures shows the round black flange that should be screwed down tight against the floor, with the top end of the black sewer pipe located in the center of it. In the picture above it, (toilet upside down), you can see the toilet outlet with the "foam donut" and sealant, which poke down into the center of the flange. The flange is screwed to the floor with the six silver-headed bolts/screws that you can see in the picture. The toilet is held down on the flange with the two brass-colored threaded machine screws that stick up out of the flange. Are you saying that this flange is raised up off the floor? Or the pipe is sticking up out of the center of the flange?
I'm not sure what the "tube" is, as opposed to the "drainpipe". Can you clue me in a little?
Bill