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What else are you seeking to do with this rig? Do you need a strong processor? Do you need a dedicated GPU? If you need decent graphics, would an APU suffice? If the answer to the second question is no, pretty much any mITX board with an M.2 slot will do the job because as you said, you can just add a card that supports eSATA with port multiplication.Then the only task is to find the smallest case that supports a board and an add-on card. The Lone Industries L3 comes to mind.
What else are you seeking to do with this rig? Do you need a strong processor? Do you need a dedicated GPU? If you need decent graphics, would an APU suffice? If the answer to the second question is no, pretty much any mITX board with an M.2 slot will do the job because as you said, you can just add a card that supports eSATA with port multiplication.
Then the only task is to find the smallest case that supports a board and an add-on card. The Lone Industries L3 comes to mind.