My understanding of the Sync Lead to SFDC flow is that it only functions the first time a Lead is sent to SFDC.
For instance, if the lead is not already in SFDC, the sync will assign it to whoever Auto Assignment Rules indicate.
If the lead is already Owned by a User, it will simply update the lead. I believe this also works when the lead is owned by a queue already.
So yes, the Auto Assignment will only run on your net new leads.
https://community.marketo.com/MarketoArticle?id=kA050000000LAAhCAO
https://community.marketo.com/MarketoArticle?id=kA050000000Kyr2CAC