Currently, when a client requests an access token for a custom scope through
https://login.microsoftonline.com/{tenant_id}/oauth2/v2.0/token
that access token's ver is 1.0. This is counter-productive because the claim iss,
https://sts.windows.net/{tenant_id}/
is not equal to the the key iss on the openid-configuration at
https://login.microsoftonline.com/{tenant_id}/v2.0/.well-known/openid-configuration
This makes it difficult to validate the token, as the receiving end of the token cannot rely on the information provided by the .well-known to validate the token (issuer in this case).
There is already documentation (on an important box) about tokens not needing to have the same version. However, there is no documentation on how to specifically ask for a v2.0 token by the client, or, alternatively, make the custom scope make the token be v2.0 by default.
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@jorgecarleitao
Thanks for your feedback! We will investigate and update as appropriate.
@jorgecarleitao You can expose a custom scope for v2.0 Access token by using below steps:

accessTokenAcceptedVersion parameter in App Manifest to 2.@jorgecarleitao I am closing the thread. Feel free to tag me in your reply if you have any further question.
@amanmcse , thanks for the tip. That does not solve the issue that I raised: that just answered my question. The issue I raised is about having that documented on the official documentation, as I outlined on the initial thread:
However, there is no documentation on how to specifically ask for a v2.0 token by the client, or, alternatively, make the custom scope make the token be v2.0 by default.
It would be useful for that documentation to be available, or at least for it to point to another URL for it.
EDIT: if it is not clear, IMO adding to the documentation makes that information available to everyone.
@jorgecarleitao I will update the document. Thank you.