Well, Saemon Havarian clearly isn't the most clean-cut & aboveboard fellow you've met in your travels, but even taking ship with him again is preferable to taking a portal that could lead gods-know-where, especially since, as it was built by your mortal enemy, it would most likely lead to a place where he would be among friends (and, by extension, you would not be).
Yes, you can indeed get back to Athkatla sooner or later, and wrap up any Chapter 2-3 quests you didn't finish. (You can even look back on them in your Journal, there's a separate "page" for each chapter of the game.)
A word of warning: (Minor spoilers, but trust me, you want 'em.) You are approaching a section of the game where you will have to spend a considerable amount of time in an area that has NO TEMPLES. Pack accordingly: Scrolls of Raise Dead and Restoration come to mind.
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Volothamp's Comeuppance
Everything you ever needed to know about the entire Baldur's Gate series......except spoilers.
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