I think that they have different servers for two reasons :-
If mac and pc players could play on the same servers then every single change made to the pc version would have to be made to the mac version before either could be released. This would just make the whole development and patch process much slower and harder. Much easer to just change the pc version and then later port the changes to the mac version without having to do it all under the same time pressure.
Also if a bug was introduced into one version but not the other which gave a "unfair" advantage or disadvantage to one of the clients can you imagine how many complaints about this they would get from the less mature members of the eq community.
So I'd imagine that they would want to keep the code identical where possible, but not be tied to making the updates at the same time on both platforms. If there are any differences in the protocols I'd image they would be trivial (Just my opinion of what I'd do if I was them - I don't actually know this)
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