What's interesting about your question is that (and I'm saying this as a Silverblue user) it's a great question, and I'm fascinated by the incredibly successful

What's interesting about your question is that (and I'm saying this as a Silverblue user) it's a great question, and I'm fascinated by the incredibly successful projects that don't even bother trying to answer it: macOS and chrome OS. Substantively, it's a difficult question to answer because there are multiple ways of accomplishing it, if I understand Vanilla correctly. In Silverblue and, I believe, macos, the operating system is a read-only image (probably ChromeOS too, but I don't know that): changing the operating system means dropping a new image on your drive, without messing with the bits that are mutable (/home and /var, in the case of Silverblue. You can layer applications directly on the OS layer in Silverblue, but it's not ideal -- though it's leading to some fascinating projects like ublue (https://ublue.it/ https://ublue.it/), in which you can branch an OS image at github, customize it to your liking, and use github features to continuously update your image so that you have a custom but immutable, auto-updating operating system.