I mean, once they both take pains to understand each other's situation and have a good, long think about it, they would find that they will agree on the big issues and be able to easily accommodate their differences. I even suspect that overall they would value the fact that certain differences exist.

EVs can, of course, be exactly the same, or differ to some degree. But - provided we restrict ourselves to humans - the basic human needs and wants are really quite consistent across an overwhelming majority. There is enough material (on the web and in print) to support this.

Wedrifid (IMO) is making a mistake of confusing some situation dependent subgoals (like say "obliterate Israel" or "my way or the highway") with high level goals.

I have not thought about extending CEV beyond human species, apart from taking into account the wishes of your example biologists etc. I suspect it would not work, because extrapolating wishes of "simpler" creatures would be impossible. See http://xkcd.com/605/.