No, you cannot check out of the Job on the mobile app if you have Checked in to the Job from Salesforce.

As of now you should check in and check out from Salesforce if you checked in from Salesforce. And if you are using the Time Tracker for Salesforce Mobile app then you should Check-In and Check-Out from the Mobile app on the device only.

We are currently working on the process to give an option to check in from Salesforce and check out from handset or vice-versa, and once it is implemented you can Check-in to the Job from Salesforce and Check out from handset.