The easiest thing to do is to store the value on the user.data object in the reconcile lambda, and then pull it off in the JWT populate lambda.
The JWT populate lambda will only be called if the authorization code grant is completed and an access token is generated, but you should be doing that in your application.
So what it looks like is:
user visits your application user clicks 'login' user clicks 'login with OIDC' user authenticates user returned to FusionAuth reconcile lambda runs, setting values on user.data user object is created JWT populate lambda runs, pulling values from user.data and calling FusionAuth APIs to add user to a group or grant them permissions on an entity user object is updated, user exists in FusionAuth