I like your diagram, it makes perfect sense to me. I see that you are working with a 3.1 system for now. My first introduction to the audiophile world was a pair of Klipsch La Scala's my neighbor had. There will always be a soft spot in my heart for Klipsch.
I would consider the Rachel (SE34i.5). I would try it monoblocked for your center channel. I would also try it out in stereo on your La Scalas to see if it would work and have enough power. If it does you could use an SE84UFO monoblocked on your center. If your plan is to migrate to a 5.1 system to a pair of Rachels and a super Zen Triode might be the ticket.
For the rear speakers I would get a cute little pair of bookshelf speakers like the Heresy speakers or a pair of Cornwalls.
I am assuming that your Yamaha has built in amps and 5.1(min) outputs. Down the road you will update to a surround processor (preamp). Look into Outlaw Audio, you can get one for around $1,000. They are well regarded and it can be dumbed down to 5.1...I read the manual.
If I ever decide to get back into home theater I would consider the Theta Digital Casablanca processor. A Casablanca V would be more than I want spend on a processor. I would start out with a Casablanca III or Casablanca III hd. Used they go for under $2k. Use it as is until I decide I like it and I am willing to upgrade it. The firmware is also upgradeable.
Why the Casablanca? Go big or go home. The Casablanca is modular. The III can be updated to a V. Ten years from now the V can be updated to an VIII or whatever model number they are on. They have been making these since the mid 90's. Since I would be connecting to Decware power amps I would save some money by reusing the older output cards that have an XLR and RCA output for each channel. I would also reuse the analog input card. That could save me some money. I would have to update the video input card and the digital input card. I might consider the cost of adding one of their six channel XLR output cards for future use.
The other neat feature the Casablanca has to offer is that you can set up presets for different "modes". One mode for Stereo, one mode for Stereo with a sub, one for surround with a sub and one without for late at night when you don't want to disturb others. Each mode can have different crossover points for your subs. One for music and one for movies. I have a 40+ page manual to read.
The Zen Ultra would be last piece in the puzzle for me. I understand what it does. I am aware of the problems it solves. I love the whole concept of what it is. It is a very important part of the ultimate system. I know you bought it first and I will not say you are wrong. You did what made sense to you. You are taking your time and doing a lot of careful research. I know there are many other surround processors out there at many price points. I would set up a surround system that would be different from yours. I would have pair of front speakers and a pair of rear speakers. For me the center and subs are optional. Because you have a pair of La Scalas you probably have them set up in a larger room and you need the center to lock the dialogue to your display. The La Scala's trade efficiency for bass response so you need a subwoofer. I hope you can get them to play nice together. It is not easy matching a sub with a pair of La Scalas.
Speaking of subs you might want to look into a distributed bass array. That involves at least four subwoofers. There is the Audiokinisis Swarm. There is another company building it under license:
https://jamesromeyn.com/audiokinesis-speaker-models/debra/That page explains everything.
Thank you for my little flight of fantasy. I have shared how I would set things up. It is on my bucket list, but I am having fun with my two channel systems for now. I do have a 20+year old 5.1 system set up in the basement. I hardly use it.
Sorry for the long post. I hope you find some of the information helpful. I know I do sometimes think out of the box, but I mostly try to be smarter than the box. I would also like to welcome you to the Decware family. Enjoy your system and the journey as it grows.