The two horizontal yellow pipes in the diagram are connecting/ leveling pipes.
Fundamentally I would want to tune each side to operate independently but acknowledge that it will be a challenge. So have the two flow pipes in anticipation of being needed.
My original plan was to turn my 125g into my sump, and toss it under the 240g. I had to rethink this when I upgraded skimmers and figured out that the collection cup wouldn't clear the gap between the stand and sump. I wanted to keep a larger sump, but without heavy modification to the stand, I couldn't get anything in there but an 84g long. With my dual 40g sumps, I could slide them through the current openings, and not have to worry about removing bracing or panels. I got the volume is wanted, and easy installation and maintenance. I see zero problem with 2 sumps.
In my experience, your "connecting" pipes should connect the 2 return pump sections. With your baffles, every other compartment should stay at the level of the baffle. Your only fluctuations should be in the return section with evaporation. Technically, each sump would operate independent from the other, except for the return sections. With this in mind, I wouldn't see a need to connect other compartments. I chose to go with 2 connections, in case one ever became clogged, but I guess 1 would work if it were large enough.
Back to the redundancy issue... I have 2 return pumps. This is because I have 2 returns. Sure, I'll have to clean an extra pump, and yes it's wear on 2 instead of 1, but I have the piece of mind that if one goes out, then the other will compensate until I can fix the problem. I've had a pump die 20 minutes into my shift, and my wife wasn't able to fix the issue. I work 12 hr shifts, so it's nice to know everything will now be cool until I get home. I also run 2 heaters. Mostly because of space, but I've found that I can set them at different temps, and basically use one as a backup for unexpected temperature fluctuations or if the primary fails. I see no problem with redundancy here. A controller wouldn't help me if I had a failure 6 hours into my 12 hour shift, as I can't just leave work to fix my tank.
As far as the dual skimmers go... if you have space for a single, higher rated skimmer, I'd go with that.
Why not use one sump for mechanical (skimmer and reactors), and the other just as a fuge? My plan is to run chaeto in one compartment and xenia in the next. Xenia will help to suck up nutrients, and I can harvest and sell it when it grows in.