The KEF Reference 1 was a speaker I was considering. However, I upgraded my KEF LS50 to the KEF LS50 Meta and heard a big improvement. Contrary to what I read online about it being a minor improvement. I have really good gear and could hear the difference.
The KEF LS50 Meta and the KEF KC62 sub will have more bass than the Refence 1. The Ref 1 will have better concentric driver. Now what is more flexible when you have room issues. I think the LS50 Meta + KC62. The room is the most important piece in your situation. Only way to eliminate the room is headphones or call Mitch (DSP done professionally).
The Yamaha NS3000 monitor will be much better than the KEF Reference 1, Magico A1, Vivid S12, Focal top end monitor. Just have a listen to the NS3000 and use that as a baseline to see if you can get better. The LRS+ is still what I would take in my office over the easier to drive NS3000. My room is smaller than yours and I am at the edge of making it sound bad.
The 3-way Reference 1 will work in your space, but I think it leave a little less margin for error than the other 2-way montors I mentioned. Though in my space the LRS+ would be best for soundstage, depth, and even bass (shocking) since it does not overwhelm.