You don't measure the length of the physical arm. What you measure is the length of the arm from the highest point to the top of the water.
So if one container is less full, then the arms are NOT the same length - the arm in that container is longer. And yes, the length of the arms changes as the water moves.
The hydrostatic pressure does NOT push the water up the arm! The hydrostatic pressure can not move the water any higher than the top of the water.
Basically, for a siphon any water below the surface essentially does not exist. You could have a mile of water - it doesn't make any difference. The only thing that matters is the relative heights of the TOP of the water.
Try it. Get a very tall container, and a short one. Position the containers so that the top of the water level is the same for both, and see what happens when you move one up or down.
So if one container is less full, then the arms are NOT the same length - the arm in that container is longer. And yes, the length of the arms changes as the water moves.
The hydrostatic pressure does NOT push the water up the arm! The hydrostatic pressure can not move the water any higher than the top of the water.
Basically, for a siphon any water below the surface essentially does not exist. You could have a mile of water - it doesn't make any difference. The only thing that matters is the relative heights of the TOP of the water.
Try it. Get a very tall container, and a short one. Position the containers so that the top of the water level is the same for both, and see what happens when you move one up or down.