After chatting with support, it seems to be impossible to deploy an AccountContactRelation record when IsDirect = TRUE, meaning the AccountContactRelation is between a Contact and its primary Account.

When I try deploying an Account record, Contact record and the AccountContactRelation record that joins them as top-level objects in the same deployment, I receive the error "INVALIDCROSSREFERENCE_KEY:You can't associate a private contact with an account.:ContactId --", presumably because in the order of operations, the Contact hasn't been updated with the Account lookup yet.

When I try splitting this into 2 deploys, deploying the AccountContactRelation alone as part of a second deployment to an org where the Account and Contact records already exist, I receive the "DUPLICATE_VALUE:This contact already has a relationship with this account.:ContactId" error, because the AccountContactRelation was automatically created due to the Account being primary for the Contact.

My organization uses multiple business-critical fields on the AccountContactRelation object, and we cannot find a way to populate them via data deploy, and have thus far resorted to manual population or separate dataloads.