Does Drupal Commerce handle MLM commission calculation?

Not natively. Layer Rules, write custom, or bridge to SaaS via REST.

Out of the box, no. Drupal Commerce is a storefront layer; it does not include MLM logic. You either layer the Rules module on top (works to about $1M GMV), write custom modules (Pattern A, works to about $2M GMV with strong team), or bridge to a SaaS MLM platform via webhooks (Pattern B, scales through $50M+). Most networks running Drupal Commerce for the storefront end up at Pattern B by the time they exceed $2M GMV; the bridge is small enough to ship in 2 to 3 weeks of developer time.