I think the main difference is that in SFDC, you can set up universal rules that apply for every single lead coming in unless told specifically to assign to someone else.
In Marketo, leads can be synced up to SFDC from a variety of sources - multiple campaigns and the Marketo Program to SFDC Campaign sync for example. If you're using the program sync, there's no way to set who it gets assigned to in SFDC - it's going to use the autoassignment rules there.
For smart campaigns which are intended to sync leads to SFDC, you would need to write the assignment rules into each campaign.
So in general, it's recommended to set that up in SFDC because there's not an equivalent of universal auto-assignment rules on the Marketo side.
I hope that helps!
Assignments in SFDC are still superior, IMO. Easier to scale.