Yes. The facility ID number is used to generate the RIN, but the RIN can be separated and used for compliance on a company-wide aggregate basis, subject to any applicable restrictions in the regulations such as regulation Sections 80.1106(c) and 80.1129(b)(6).
Question and Answer was originally posted at: Questions and Answers on the Renewable Fuel Standard Program (PDF) (55 pp, 221 K, EPA420-F-07-041a, August 2007, About PDF)