Hello Konstantin,
I have few questions for you here. If you put back original AMI BIOS for your board, does it wake up from S3? I do recall that you have kind of proprietary platform which does switching/routing, and does have only Coreboot ported. Am I correct?
AMI BIOS would be preferable starting point for debugging/testing of this problem, but if it does not exist, we'll try something different, with help of sticks and ropes down the road. Do NOT forget, as I also recall that you are using very old version of Coreboot: coreboot-4.0-8341-g5e6dd5f-dirty Thu Mar 19 10:15:27 UTC 2015.
I have another suggestion for you: to try to go to S4 (hibernation) sleep, and then to try to wake up? Does this work?
I need from you Linux kernel (preferably Fedora 24/25) S3 and S4 logs. How to achieve this? If the whole platform does not wake up, simply do the HW hard reset, and then, after booting up capture previous log with the command: journalctl -b -1 , and attach it to the email.
Zoran