Using the Auto-Assignment (Lead Assignment) rules in SFDC is recommended rather than creating assignment rules in Marketo.
Since creating assignment rules in Marketo is difficult to maintain, I recommend marketers focus on marketing rather than maintenance.
Lead Assignment rules only run on initial Lead creation, you can’t run them again for existing Leads. Thus, if a SFDC Lead or Contact flows through the Sync Lead to SFDC flow step and the Assign To is set to --Use Auto-Assignment Rules--, Marketo will sync any field updates but will not run the record through SFDCs assignment rules again.
If you need to run Assignment rules again, have your SFDC Admin create a custom trigger and flow in SFDC.
The SFDC Lead Assignment rules may required that specific fields be populated. Check with your SFDC Admin.
Here is an interesting idea about enhancing how the flow step works.