I was saying that having /v2/ in the URL implies all of the endpoints will have a /v2/ and that they will be part of a matched set. Having it in the header makes for having version numbers that are targeted at each specific endpoint without making it look like the others are affected.
Here specifically I was suggesting that the /v2/ in the URL would make people using the API more likely to set the /v2/ in their app to use it across all calls rather than different per endpoint versions.
It looks like the calls are in the version rather than the version being in the calls.
I see it a bit as a REST thing: /v2/some/endpoint implies that v2 "owns" "some/endpoint". What state does "v2" represent? Does it own every "some", just "some/endpoint"? What is that hierarchical relationship really?
It's a general problem I see with any REST API that tries to version that way. Version isn't a strict hierarchical "owns" relationship and embedding it early in the URL sort of violates REST principles in what the folder path of a URL is meant to imply. (Admittedly, that's a bit of a more strict interpretation than most people pragmatically follow when building REST APIs, but it is an interesting and useful strict interpretation so worth bringing up and examining.)
If you are versioning individual endpoints it might make sense to use URLs like: some/endpoint/v1 and some/endpoint/v2
That makes it more clear that "some/endpoint" "owns" that relationship and kind of/sort of what "exactly" is being versioned. If you must put a version number in the URL.
That said, REST has always been about content negotiation as a long held tenet, and that has always been about using the right Headers (since the earliest HTTP 1.x apps), and I've always felt like complaints that you can't send the right version Header reflects primarily on bad tools that don't understand HTTP (and REST) as well as they should. Sending Headers is an important part of HTTP. I don't think it should be harder to send the right Headers than to embed things that would be Headers into the URL. Though that's just my somewhat strong opinion on the subject.
But now I think that the versions are not part of the resource path, just as starting the path with /api doesn't mean the API is part of the resource. The versions are part of the api path. If I had a URL that was /api-v1 and /api-v2 it would be more obvious, perhaps, that the URLs are addressing different API implementations, and everything that came after was the RESTful bit. Having /api/v1 and api/v2 as the prefixes isn't quite as clear on that point, for sure.
The reason I like having the version in the path is it makes it a bigger deal for the implementer when they're making breaking changes. Having a per-endpoint, slightly hidden way of versioning endpoints might mean it's harder for them to intuit quite how many changes are flying at their API's consumers.
I've also argued against /api for similar reasons under "strict REST", too. It's often "redundant" information not all that useful in the URL hierarchy. Everything is an API. There's no "non-API" endpoints. Even pages that only return HTML are a public API. But I also understand the usefulness for things like security audits to have a magic circle labeled /api even though that magic circle doesn't really do anything.
I think you are almost assuming the implementer doesn't abstract the URL routing in some way and has to care about about every possible URL route? In practice there is often very little difference on the implementer side between routing `/api/v{id}/some/route` and pulling in the version number as a route parameter and picking up a version number from a header. The implementer is still just seeing a version number parameter injected either from their routing framework or their header dictionary. In both cases the amount of code they see is roughly the same. In many cases all "versions" of the code might only be a single "Controller". Outside of a few languages such as PHP there's few languages that have a direct 1:1 between URL paths and "Controllers" or "Source Files" or anything resembling that. At some point there's always some intuition that side-by-side versions imply side-by-side code and the "tech debt" sense of that maintenance version, but that intuition comes from numbers of classes and size of classes and indirect measurements like PR cycle time and Sprint planning estimates, and is never directly connected to URL routing versus Header negotiation. (Again, in modern languages with modern routing frameworks. Obviously if you have to drop a PHP or ColdFusion file for every API endpoint you'll feel URLs a lot more painfully than that.)
In reality it's probably completely equivalent. The version prefix in the path would probably live in some GITHUB_API_URL variable. The header would be set on the http session object.
You can update each endpoint in non-backwards compatible ways without having to update all of them.
If you have it in the URL, it's likely libraries and custom scripts will just set the value in configuration instead of per-callsite.
You don't want to have to wait to fix up some API or make non-updates on all the rest just to release a new version.
edit: I agree that making it optional is a bad move