I think that my sata port is also 6Gbps since that consulting the specs I find that the link speed is 6Gbps but the negotiable link speed is 1.5Gbps. Can you confirm if it is indeed a sata 3 port?
The optical bay may show 1.5Gbps if the optical drive is still there because the device probably couldn't pump out data any faster anyway.
On my mid-2012 13" non-Retina, the optical port does 6Gbps and it has done so reliably (at least I haven't noticed any difference) since I got it in 2015 (they produced the 13" mid-2012's until early 2016). I just checked again and both ports (Evo 850's on both) have a negotiated speed of 6Gbps. OWC originally said the 2012's optical got 6Gbps (2011's mostly didn't) but then added a warning later. I don't recall anybody saying they couldn't get 6Gbps on the optical port on this forum.
My opinion is that changing the drive in the optical port was easier than changing the HDD. YMMV.
There are problems with the HDD cable on this model. It may work with a HDD but not with a SSD. You should replace the cable at the same time. The bracket that is used to fit a 2.5" disk into the optical port has electronics. If you go this route, you can buy a more expensive one like the OWC Data Doubler or buy a cheaper one from a place that has a good return policy - it seems that with the cheaper ones, if you get one that works (chances are good that it will) - it will work consistently after that.