I'm glad that you were able to resolve your issue and thank you for posting your solution so that others experiencing the same thing can easily reference this! Since the Microsoft Q&A community has a policy that "The question author cannot accept their own answer. They can only accept answers by others ", I'll repost your solution in case you'd like to "Accept " the answer.
Once you specifically added the following to the application manifest, under access, id and saml, the appropriate auth context values in the acrs claim started getting sent passively in the user's JWT if the conditional access policy was satisfied.
{
"name": "acrs",
"source": null,
"essential": false,
"additionalProperties": []
}
Thanks,
Akshay Kaushik,
Please "Accept the answer" (Yes/No) as this will help us and others in the community as well.