I saw a comment in my email that seems to have been deleted and figured we should answer this one since it seems we missed it.

At this point code-server and upstream's server are almost identical except code-server makes things more friendly for self-hosting.

For example things like the ability to host at sub-paths as mentioned, self-contained web views that do not call out to Microsoft's servers, the ability to add your own marketplace, collect your own telemetry, and some other things.

Some of these changes appear very unlikely to ever be adopted by Microsoft (marketplace, telemetry, allowing all extensions to use proposed API by default, some other changes probably) but some I expect to make their way upstream, further closing the gap. But at the moment it looks like there will always be some subtle differences.