Yes, there are no atomic upgrades. Even when a static binary is replaced, there are many instances of it running and the processes aren't restarted atomically.
However, in a protobuf-based system within a single organization, you can at least say that every deployed binary expects an API that was defined by some version of the same protobuf file. At Google there is (or was - it's been a while) a linear history of this file in source control somewhere. That limits the possible API variations in existence.
By contrast, in the acko.net article, he describes the ad-hoc variation that happens when many organizations make their own extensions to the same protocol, with little coordination with each other. (And yes, the web is like this too.)
However, in a protobuf-based system within a single organization, you can at least say that every deployed binary expects an API that was defined by some version of the same protobuf file. At Google there is (or was - it's been a while) a linear history of this file in source control somewhere. That limits the possible API variations in existence.
By contrast, in the acko.net article, he describes the ad-hoc variation that happens when many organizations make their own extensions to the same protocol, with little coordination with each other. (And yes, the web is like this too.)