I think u might be right. My main drain is connected to the roller mat with tubing. When I took apart my drain to inspect my gate valve, the tubing on the barbe fittings just slipped off and that was right at the water line.I have a similar setup on my IM 100gal bean animal using a ClariSea 3000 gen 3. Modified sump from filter socks to roller mat. I experienced everything you were talking about BUT it got a lot better when I got rid of two 90 elbows on my main drain going to the roller mat. I finagled some 45s and soft tubing instead.
I also find that making sure the seal between the main drain and roller mat is tight is important. For example when I take out the roller mat for maintenance and put it back if I didn't have a tight seal between the main drain and the roller mat elbow then I was getting too much flow through the secondary and it would throw every thing off.
Till this day things will be whisper quiet and flowing perfectly and then randomly I'll have super high water level in the DT and water gushing out of the emergency and secondary and I feel like I'm going in circles adjusting pump speeds, gate valves and messing with the ATO and I usually end up coming back to the roller mat and that will end up being my adjustment. IE it was being bypassed, or stopped rolling so the fleece is clogged more then usual but not completely clogged
Hope this helps.