During a remote session with a customer, a comparison between the source and target databases revealed a discrepancy in the indexes. Specifically, while the source database contained three types of indexes (PK_xxx, IX_xxx, and NCI_xxx), only the manually created PK_xxx and IX_xxx indexes were visible in the target database after restoration. The absence of NCI_xxx indexes prompted an investigation into the BACPAC export process.
This meant that the BACPAC file didn’t have the set of recommended automatic indexes. Click through for the explanation, though I’m not sure there’s a good way to fix it, short of manually scripting out those automated indexes yourself.