There might be runtime flags that affect performance. In particular there may be feature that are being A/B tested chrome. Content shell uses the flag values defined in testing/variations/fieldtrial_testing_config.json, while chrome builds get their variation configs from a backend service that manages our A/B testing framework. Also, some of the command line flags have different default states in content_shell vs chrome.
Since you are noticing a difference in graphics performance (probably), the first thing I would do is compare the contents of the about://gpu pages on the two browsers. Do you see any difference? The speedometer benchmark uses 2d canvas heavily, so pay special attention to anything related to canvas on the about://gpu page.