In terms of your second question, the Right to Financial Privacy Act would not apply to a search warrant received from a local police department because the RFPA applies only to requests for customer information from FEDERAL government authorities. You would instead look to your state statutory law and cases for guidance on what you can disclose and how.
In terms of your first question, there really isn't a discrepancy between those provisions. The first, in 3403(b), is the general rule that the certificate of compliance must be provided. The second, in 3411, is a specific requirement that directs financial institutions not to delay in gathering requested customer information pursuant to an administrative or judicial subpoena or summons. These are the types of records requests where the federal authority must (unless an exception applies) give notice to the customer and an opportunity to challenge. Once the notice and challenge time period has passed, and assuming any challenge is unsuccessful, the federal authority should provide a certificate of compliance and the institution should immediately turn over the records. The main point of the 3411 procedure is that the institution should not wait until the challenge period expires to begin the compilation and research.
The timing is different on federal search warrants, for example, because the government is only obligated to give after-the-fact notice to the customer and there is no right to challenge, so there is no preliminary notice and challenge period.
Always look at the particular type of records requests (subpoena, summons, search warrant, formal written request, or other), then review the exceptions, then pigeonhole the request even more narrowly (if, for example, it is something exotic like a request from the Secret Service in the exercise of their protective function, or something else that has special provisions relating to it.) Once you have narrowed down specifically where it falls within the RFPA, you can determine whether or not you have a right to require a COC and when you should get it.