Are you sure rival will work with a 40-26 crank even if the rings are the right size? I'd check that. You may either have to go with bigger chainrings like a 46-34 or a different shifter/derailleur setup to accommodate the little rings.
I have mechanical disks (BB7's) on one of my randonneuring bikes and they are easily my least favorite component on that bike. They always squeak, and I constantly have to adjust them. If I ever get disks again, I'll suck it up and get hydros, but honestly, I'm completely satisfied with rim brakes for randonneuring so it's extremely unlikely that my next bike will have disk brakes at all. Seems like you’ve already made up your mind about that, so I’d go hydro. It’s only money, you’ll make more. It’s not like this is turning out to be an economy build anyway.
I also don't like the aesthetic of ergo handlebars, so I'd go with something else. I prefer compact drops with brifters since I seem to spend more time on the hoods than with bar-ends. I have nitto-M151F’s on my only brifter bike, but that has a quill stem so I needed a small diameter bar. There are tons of options available in 31.8. Handlebars is a pretty personal thing so you'll have to figure that one out for yourself. Rando bars could work for you since you like to tilt the brake hoods in, just find some without an egro bend. There are several out there. I have Nitto B135’s on my fixed-gear and like them a lot. I wouldn’t worry so much about the diamete. Threadless stems come in different handlebar diameters or you can easily use adapters to size up a smaller bar to a bigger stem. It’s not an issue, so just look for some that have a shape that you think will suit your riding style.
I don't see the benefit of running tubeless tires for randonneuring, but I guess more and more people are going in that direction and seem satisfied. Flats are pretty rare for me or brevets. I think I had 3 last season, and I’ve had seasons with zero. I run compass EL’s and can replace a tube in under 5 minutes, so I just don't see any reason to bother with tubeless. I was on a brevet last year with a guy riding tubeless who got a flat and there was sealant all over his bike and clothes, and it took him over 30 minutes to put a tube in there and get going again. I can just imagine how long it took him to clean up that mess when he got home. No thank you. I get it for off-road, but for brevets tubeless solves a problem that I just don’t have.
I also wouldn't recommend that VO rack you have in mind. It either fits on your bike or it doesn't. I bought one and it didn't fit so I sold it on CL and bought a Nitto M1 and a Nitto Zao decaleur which works better for my bike. Racks and decaleurs are tricky because there’s really no way to tell for sure how they’ll fit on your bike until you actually install them, at which point you’ve already bought it. The Nitto racks have a lot adjustability while the Zao decaleur has none.
As long as I'm nit-picking, I like A-600 pedals better than the M540’s you have picked out. Although I’m mad at Shimano right now, I still think SPD is the best clipless choice for randonneuring all things considered.
I love the WI rear hub you have picked out, but I’ll encourage you again to check out the VO rear hub. Definitely not as sweet as the WI hub but probably good enough and field serviceable with no tools which means you can replace a drive side spoke without any tools other than a spoke wrench. Just something to think about. I built a new wheelset this off-season and went with the VO hub for that reason, and it's a lot cheaper than the WI hub. OTOH, I’ve never broken a spoke on a brevet so there’s that.