Hi Chad. Firstly apologies for the delayed response on this.
The filters set via SQL Source Control should be honoured by SQL CI. If you are finding this is not the case, please raise a support ticket via support@red-gate.com and we'll see if we can help.
With regards to the options, we debated at length whether they should be set once in SQL Source Control and then honoured by all the tools (SQL CI and SQL Release). We decided not to in the end because there were several cases where options suitable for one environment did not make sense in other environments (inclusion of tSQLt tests being the best example). We also thought that a release manager or DBA might not be happy if an option change made by a developer in SQL Source Control changed how a production deployment functioned.
Do you find that you use exactly the same options in both SQL Source Control and SQL CI? Do you use SQL Release and if so do you use the same options there? Would be interested to hear your thoughts. You're welcome to email the team regarding this at dlmautomationsupport@red-gate.com

I can save a standard set of filters and compare options as part of the source control tool. Have SQLCI use those as part of the compare process