What does enabling containment on server incur?
Instance-wide settings are typical when the database engine can optimize code paths if the setting is off.  In this instance, having contained database authentication = 1 means the database engine must perform checks on each database that it normally wouldn't need to, in addition to checking login requests against any database that has containment enabled.

The real impact on this is probably quite negligible; if you are forecasting that at some near-term future point you might need to enable containment for a specific database, you may consider enabling the instance-wide setting during some maintenance window.