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Wait, all your servers are the same?
For the root partition, pretty much, yes.
Custom per machine software is outside of the centrally managed root partition, and therefore does not interfere with updates.
Software run by the server can be run in a chroot with a limited view of the root partition, allowing the application to be hermetic and therefore protected from changes on the root partition.
We also have support for multiple libcs and use static linking for most library applications.
This combination makes it easy to have hundreds of different apps with their own dependencies that change at their own pace.