I'm not in knowledge of developing or engines but i noticed that actions that increasing or decreasing some number (building/destroying/capturing/repairing, gathering resources, hitpoint decrease due attack/increase due healing) counted by engine at immediate time and right at these times fps are decreased. However in other similar games all actions that changing these numbers counted at a certain time like between a second or two. I think this must be tried to see result.
Also there is something wrong with the unit movements in formations and routes that causes fps decrease as everyone can notice.
By the way i dont use any mods and i knew this game before years and noticed it. Its a theory of course.