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Normally I would say software, or rather a raid-like filesystem like btrfs or ZFS. But in your specific case of funneleing it all through a single usb-c connection it is probably better to keep using an external box that handles it all internally.
That said, the CPU load of software raid it very small, so that isn't really something to be concerned with, but usb connections are quite unstable and not good for directly connecting drives in a raid.
I mean I've been running the setup this way for >4 years and never had any problem with the USB connection, so I cannot attest to "usb connections are quite unstable"...
I supposed that is because the JBOD box was handling the raid internally so short connection issues are not that problematic and can be recovered from automatically. But that wouldn't be the case if you connected everything together with a usb hub and usb to sata adapters and run a software raid on that.
I don't know usb c in thunderbolt has direct access to pcie lanes.