@takitaj Thank you for the post, lots of very good information there!
I just want to clarify a few things since I think I created some confusion with some of the pictures I originally posted. I apologize for that and it is fully on me.
I do have a riser on the emergency drain in the overflow box. It is the red one included with the eclipse overflow. Through leak testing, I have consistently run the overflow with a slight trickle down the emergency drain. More recently, I have been running more than a slight trickle as an experiment to see if it had any effect on the main issue.
The main issue I am worried about is that I can set the gate valve so the water level is perfect in the overflow box. Just a slight trickle down the emergency drain. Then everything will run fine for a while. Eventually, the issue appears in that the overflow level is suddenly sucked down over about 30 seconds span so that the main drain is sucking air. About five minutes later the water level has risen and everything is running as it should - full siphon on the main drain, slight trickle on the emergency. About 30 minutes later the cycle repeats - water level drops quickly then rises back and runs as it should. This only seems to occur at pump power levels above 40% and is intermittent only occurring randomly. I work from home so I have been watching it run for the past week and have been trying to tweak the valve to avoid it. Some days I never see it, other days I see it a bunch even if nothing changed from the previous day. Today for example I have been trying to induce it to grab a video to post and it hasn't happened yet. Thursday, on the other hand, it was happening extremely frequently and was driving me insane. I will give the method of running the main drain wide open for a half-hour before slowly closing a try to see if that helps.
The secondary issue I am having is noise. The main source of the noise is the water falling into the weir box. To try to reduce this I have tried running the overflow water level higher which helps some. However, if it gets too high the emergency drain takes too much flow and gets loud. I also don't think using a longer riser on the emergency drain is a good idea since the eclipse box seems to be designed too short. If I close the main drain all the way (to simulate a clogged drain) the emergency is not able to achieve full siphon due to sucking air for the surface and the water level rises dangerously high as shown in the picture below.
In regards to the sump level baffles. I apologize for not clarifying that this tank is going to be a "high-tech" freshwater planted tank. As such I don't need a constant water level for a skimmer. I was actually originally planning to use a more traditional sump design with baffles. However, since I am running CO2 injection on this tank (the filter housing attached to the return is the reactor to dissolve the CO2 gas), I decided to go with a baffle-free design to limit splashing in the sump in order to reduce CO2 off-gassing (CO2 can get costly...). I don't see any issue with not having baffles in this specific circumstance but I may be missing something?
The sump water level is something I am very conscious of since I live in an apartment. As a result, I have carefully watched and planned to ensure the sump will not overflow. The first picture below shows the sump at the maximum allowable level during pump operation. The second picture shows the sump with the pump stopped after the overflow and return lines have all drained. The main display tank water level drops very little when the pump is turned off due to having the overflow flush with the top lip and having the return siphon break right at the water level. During the real operation, I will likely run the water level a bit lower as an additional safety net. I do plan to get an ATO as soon as my budget allows. Until then I will be manually topping up with distilled water if evaporation is significant enough to require it (large water changes will be performed weekly so I might not need to).
Once again I appreciate all of the replies and advice and apologize for any and all confusion.