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What would be the benefit of a thunderbolt to PCIe enclosure with an HBA SAS SSD card inside, instead of just a regular external thunderbolt SSD drive? Apart from many thousands of dollars of course.

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The point would be to have an enclosure of several/many SAS HDD's that you want to connect. The Thunderbolt to PCIe enclosure holds the PCIe card only, and a separate SAS enclosure holds disks. (The spinning rust type, surely.)

People also connect LTO tape drives using this interface.

Having many SAS drives on the end of a single Thunderbolt connection completely defeats the point though. whats the point of the fast PCIe link and the fast SAS drives when you are bottlenecking them all on a single thunderbolt cable?

I think you're off base regarding the speeds attainable by Thunderbolt (and/or the speeds of hard drives). Feel free to peruse e.g. https://www.sonnettech.com/product/thunderbolt/pcie-card-exp... ; https://docs.broadcom.com/doc/12353459 (on PCIe and SAS bottlenecks).

Besides that, whether a throughput limit defeats the point depends on what the "point" was to begin with, as well as what the alternatives are.

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