Some employers will separate your cover letter from your resume and have different hiring managers look at the different pieces. (flexjobs.com)
These companies all have applicant tracking systems that require individual applications with separate cover letters for each position, and I do meet the requirements for all the positions I'm applying for (entry - level positions in different departments, essentially). (careerdigital.com)
Separate Cover Letter formats are available for mid level jobs which are mostly Managerial in nature. (template.net)