When the ForeignKeyMode.None setting is used and the schema is updated using DomainUpgradeMode.PerformSafely, the indexes for foreign keys are created, despite no foreign keys are created. They shouldn't. Alternatively, an IndexMode could be introduced to fine-tune automatic index creation. This is especially important in scenarios where FKs and indexes need to be hand-tweaked for the sake of performance (e.g. when partitioning is used).
Before running a schema update:

After running a schema update:

Note: Anything starting with ext_ is ignored using an IgnoreRule.