After some testing this is my experience on an early 2009 iMac 20" with 8GB RAM and Samsung 860 EVO 250GB (MZ-76E250B/EU):
* When Samsung SSD is placed in the Optical Drive bay and the computer boots up from its genuine mechanical hard drive installed on it, so SSD acts as slave drive, the reported negotiated speed is 3Gb. Always.
* When Samsung SSD is placed in the Optical Drive bay and the OS is installed on it and the computer boots from it, so SSD acts as master drive, the reported negotiated speed is 1.5Gb. Always.
* When Samsung SSD is placed in the mechanical hard drive socket and the OS is installed on the SSD drive and the computer boots from it, so SSD replaced the mechanical hard drive, the reported negotiated speed is 3Gb. Always.
The testing was done on a clean High Sierra install through dosdude1.com software. The file system on the SSD was APFS and as the machine didn't support native APFS booting it was needed a workaround to boot from the APFS SSD. The mechanical drive was formatted with HPFS+ and had a genuine El Capitan installed on it, but was an upgrade not a clean install.