Marketo's tracking of Sent, Delivered, Opened and Clicked is totally independent of SFDC if the emails are being sent from Marketo. Delivered may not mean that recipient actually received it, especiall if a Soft Bounce activity follows it. Opens are dependent on the recipient displaying images. If they do not display images, they can open and read your email, but it will not be shown as an Open. Clicks are definitive - if a recipient clicks a link in your email, it will be displayed as a Click in Marketo.
Clicks on the standard unsubscribe link (e.g. [cname[.[your domain]/unsubscribepage.html) should not be counted as a click, but a click to a prefernce center will be included in the click count in the email performance report.
Do you have a specific example of a discrepancy between Marketo and SFDC that you need help understanding?