I use motherboard ports first and don’t install a HBA unless needed, because it consumes a lot of power and prevents cpu idle
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I trust MB SATA more in terms of reliability. HBAs tend to overheat too.
However, if RAID topology allows, I'd try to spread the drives such that either one of MB or HBA failing completely would not bring the array down (RAID10 with 1 HBA, or RAID5/6 with 2 HBAs).
I've heard a few horror stories of LSI HBA's causing some serious data corruption. Most of these cases were due to insuffiencient airflow. When it comes to data integrity I wonder if LSI HBA's in IT mode have more or less ability to detect errors or increase/decrease the risk of data corruption?
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Depends on your configuration.
If you do not need to passthrough the whole HBA to a VM for example, then, just go with the most convenient way for you.
on my mobo and cpu, I use the hba first as theres more bandwidth. mobo sata last as one of my two nvme ports runs through chipset and chipset to cpu is limited bandwidth, roughly 4GB/s total so sata and one nvme competes for that.
if you have a cpu/mobo thats made in the last year or two you would have more speed for that interconnect and its not that big of a worry.
I bought a cheap HBA because then I can virtualise the PCI-e card to a VM and use it in ZFS.
Granted I could probably do the same with an onboard SATA controller, but I have more faith in a dedicated controller for my array.
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