I believe there are some misunderstandings here.
The onboard SAS/SATA capable controller (or SCU, SAS Controller Unit) is either in RSTe mode or ESRT2 mode. There is no AHCI mode for SCU ports.
RSTe mode does support pass-through, which means if you have a drive connected and you don't have any RAID configurations, OS can see the drive directly. While ESRT2 doesn't support pass through, which means if you don't configure a drive as RAID volume, the OS won't be able to see it.
For OS to see a pass through drive under RSTe mode, RSTe driver is still needed. We don't have any RSTe driver for Linux, but as mentioned in the Intel® Rapid Storage Technology enterprise (Intel® RSTe) for Linux OS document:
SCU is the Intel® Serial Attached SCSI Controller Unit that is part of the C600 family Platform Controller Hub. The Linux SCU driver (isci) has been upstreamed to the Linux kernel since kernel version v3.0. However, the latest Linux kernel is always recommended to get the latest bug fixes and features.
So you may want to check your kernel version. You can also install Windows on RSTe to confirm whether the issue is caused by drive firmware.