Makes sense, thanks for the details!
I recently got my Turris Omnia and tried it with Init7
I updated to the latest firmware and that didn’t help me, the problem with SFP still appears to exist.
omnia 15.05 r47055 / LuCI 7d1985286660e6db4b662c9f5c4cdadf985a3d69 branch (git-17.009.29435-7d19852)
I have sent the email to Init7 asking them to disable auto-negotiation.