Why is the Primary Contact field on the Opportunity in the Nonprofit Success Pack different than the donor?

When a Donation Lead record is converted to an Opportunity (aka Donation) record, your Soapbox Donations for Salesforce packages add a Contact Role record in the Contact Roles related list for the donor. The Role is set as "Donor" and the Primary checkbox is checked.

Depending on your NPSP Settings, the Primary Contact lookup field on the Opportunity may also be populated. This is not done by your Soapbox Donations for Salesforce packages but rather the Nonprofit Success Pack itself. The Contact used to populate this lookup for Household Accounts is the Primary Contact from the Household Account. In many cases, this will be the same individual as the donor. In some, it will not.

If you wish, you may manually update the Primary Contact lookup field to match the Contact with the Contact Role of "Donor" marked as Primary on the Opportunity.