Civilization 5 – Does Accuracy Work Against Naval Units?

Correct, they are not necessarily the same. You will receive a random technology from those that are available to you, and they will receive a random one for them. This does imply that if you are making use of research agreements, you should try not to "skip" techs that are cheap, since you want the research agreement to give you something as "expensive" as possible.

I can confirm that embarked land units do get an extra two movements under Elizabeth's special ability.

I just tested it in two saved games, one with Elizabeth and one with Augustus. An embarked land unit in the Elizabeth saved game had six moves, but Augustus' unit only had four. Both had Astronomy (+1 embarked movement, embarked units can move over ocean) and Steam Power (+1 embarked movement).