I think this is something the OS can override. If I remember correctly I could discover a hotplugged SATA device in Windows by using "Scan for new hardware" in the Device Manager.
More specifically, the system's firmware AHCI hotplugging configuration only applies to the system firmware.
That is to say, if hotplugging is disabled on your SATA controller, then the firmware won't see a new SATA drive if you plug it in while the machine is running. So, for example, you won't get a UEFI boot menu entry for it if you go to the boot override section that presents all of your storage devices.
Once the operating system takes over, that's all a moot point. Whether hot-plugging was disabled in your firmware settings or not, if the OS supports it, it will work. Both Microsoft's AHCI driver (msahci.sys) and the Linux "ahci" kernel module (or built-in) support hot-plugging.
On my Windows desktop with an Intel SATA chipset, hot-plugging a drive did cause Windows to briefly drop all other drives on that controller before re-enumerating all of them, which lead to a BSoD because one of those drives was the drive with Windows itself on it. However, this was solved by installing Intel's chipset-specific driver (Intel Rapid Storage Technology, iaStorV.sys) and tweaking the registry to have that one start at early boot instead of msahci.
I think this is something the OS can override. If I remember correctly I could discover a hotplugged SATA device in Windows by using "Scan for new hardware" in the Device Manager.