Hey @Shawn_Optipath 
First off, thank you for taking the time to run such a careful experiment and write it all up. This is genuinely the kind of feedback that helps us get better, so it really means a lot. I've gone ahead and moved your topic to Discussion so the community can keep chiming in.
You're totally right to flag this. Asking Assist to "add one component, touch nothing else" and then seeing three others move (one by hundreds of pixels) is frustrating, and I completely understand why the quiet, easy-to-miss changes feel unsettling in a bigger app. Wanting to trust that a change stays scoped to what you asked is completely fair.
On questions 1 through 4, I'd like to check in with our engineering and product teams so I can give you confirmed answers. Give me a little time and I'll follow up right here.
As our attention shifts to the new app builder, improving Assist specifically inside classic apps isn't a primary area of new investment for us going forward. A lot of our focus right now is naturally going toward the new builder. What I can commit to is that classic apps themselves aren't being left behind: Timofey from our product team shared that we're supporting classic apps for at least two years from when the new app builder reaches GA (it's still in beta today), and during that time we're investing in the new builder and its classic apps conversion experience, so that over time you'll be able to successfully re-create, and in some cases perhaps even improve, your existing apps. 
You can read his note here:
And to everyone else reading, please keep the feedback coming! Detailed write-ups like Shawn's are exactly the kind of feedback we love to see, so if you've hit something similar or have thoughts to add, we'd love to hear them. 
I'll follow up here soon!