SQL Source Control v3.0.5.7 allows you to configure the same comparison options available in SQL Compare's Project Options dialog.

Comparison options can now be set via a configuration file in you database repository's Working Base folder. The following Knowledge Base support article describes how to use this configuration file:
http://documentation.red-gate.com/display/SOC3/Setting+SQL+Compare+options+in+SQL+Source+Control

The plan in the future is to provide an options dialog to allow you to configure the comparison options that are changed most often, but we believe this configuration file procedure should help users in the interim.

I've added this idea to UserVoice to gauge the demand for a dialog for these options - so please vote if you'd like to see this dialog added to the product!