Great looking setup!
On a bean animal overflow configuration, Synergy, Modular Marine or other, Flow from the overflow box to the sump should be nearly silent. Main drain (with gate valve) should be totally submerged in the overflow box and exit just slightly, maybe an inch, below the water level in the sump and be carrying 100% of the flow. Secondary drain should be just a hair above the water level in the overflow box so that any rise in the level due to blockage of the main drain begins to flow through the secondary. Emergency should never carry water unless both the main and secondary become blocked.
To me, looking at your top-down view of the overflow box, it looks like either the main drain is too high or the secondary drain too low. You need enough difference in height so that the main drain can fill completely and carry all the flow with a little freeboard to spare before the secondary starts to see water. The way yours is set up, it looks like the secondary drain will be carrying water when the box level is high enough to allow the main drain to siphon. This would contribute to flow noise and may be the reason you extended the secondary drain pipe. If what I am seeing and describing is right, you may want to raise your secondary drain in the overflow box.
Here is what I would check:
1. Is main drain running at full siphon, not pulling any air? Answer should be "yes". If "no", close gate valve slightly until main siphon is completely submerged.
2. Is secondary drain flowing water? Answer should be "no", although a tiny, silent trickle is acceptable and preferred by some as a reference for how much flow the main drain is carrying. If "yes", raise the secondary siphon above the water level at which the main drain holds full siphon.
3. Is there any flow from the emergency drain? Answer should be "no".
When all is adjusted correctly, you should be able to achieve a near silent aquarium. The loudest noise from my tank is the cooling fans on my lights and a faint hum from the pump if I open the cabinet. Water noise is undetectable.