Does CBP have to provide an accommodation that would violate a seniority system or collective bargaining agreement?

No.  A proposed religious accommodation poses an undue hardship if it would deprive another employee of a job preference or other benefit guaranteed by a bona fide seniority system or collective bargaining agreement (CBA).  Of course, the mere existence of a seniority system or CBA does not relieve CBP of the duty to attempt reasonable accommodation of its employees’ religious practices; the question is whether an accommodation can be provided without violating the seniority system or CBA.  Often the agency can allow co-workers to volunteer to substitute or swap shifts as an accommodation to address a scheduling need without violating a seniority system or CBA.