eSATA is about more than just hot-plug:
It uses a more robust connector, longer shielded cables, and stricter (but backward-compatible) electrical standards. The protocol and logical signaling (link/transport layers and above) are identical to internal SATA. The differences are:
- Minimum transmit amplitude increased: Range is 500–600 mV instead of 400–600 mV.
- Minimum receive amplitude decreased: Range is 240–600 mV instead of 325–600 mV.
[...]
This, including making the devices appear removable, is what the BIOS option is about. As indicated, the changes are backward-compatible.
Apparently, ASUS decided that two options would be too confusing. Also, BIOS setups are sometimes just plain terrible.