Are two-step step-up rods interchangeable with three-step rods? Are the pistons the same length? Does it matter if the cover is domed or flat?

The two step and three step primary jets are not alike, the rods need to match the jets, in the front.
AVS carbs. used the three step rods and jets a lot
I use to have carter AVS jet kit and let it get away

You can convert it, but you need the matching top plate, piston also. Pretty sure the jets are the same.

There were different pistons in some MOPAR type AFBs, but the standard piston is the same. For three step the Primary jets are taller, the rod is longer, and you use the cap with the protrusion. Spring rate was the same for most mopars. So that allows the rod to operate over a longer range and use the intermediate step.
If you're going to two step use the early standard jet (shorter), the 2 step rod and the flat cover.