You are implementing Dynamics 365 Customer Insights - Data as your company's Customer Data Platform.
The initial dataset tables contain contacts from Dynamics 365 Sales. Commerce customers, and service management platform incidents.
In your first unification run. you set Dynamics 365 as the primary table but only see eCommerce profiles that were able to be matched with Dynamics 365 contacts. You need to ensure that unmatched eCommerce customers are also added as a profile in Customer Insights - Data Solution: Make eCommerce customers the primary table in the match step.
Does this meet the goal?