Issue #24585: Enables build-to-build upgrades that preserve settings.

Rather than using Burn "Persisted" variables we now add registry keys for each added feature. These can be detected by the installer regardless of which version installed them, and we use this for Modify and Upgrade. In particular, Upgrades can't access the Persisted variables, but can find well-known registry keys.
There are also some changes to the bootstrap app to properly handle upgrades.
Finally, a few minor improvements to the Windows build to keep things tidier.