The whole point of an ATS (applicant tracking system) is to filter out as many candidates as possible so that only a very small number of "perfect match" candidates remain for further consideration. It works on the assumption that ideal candidates have all the "right" keywords and format in their resumes, the "right" amount of experience, the "right" degree, no gaps, nor weird career paths, etc, etc. Do such screening/tracking practices actually deliver?
The fact is many jobs are not filled by people filling out a form on a website, uploading their resume, and crossing their fingers. Many jobs, especially really desirable ones, are filled by people exercising their professional contacts, by referrals, or by professionals reaching out to other professionals who are interested in the work (and not HR functions).
If you know who the hiring manager is, it doesn't hurt to contact them directly with a personal note introducing yourself, why you're interested in the position, and a compelling case for why you're the one for the job. You don't have to mention anything about the ATS when you contact the hiring manager. The worst they will do is ask you to apply through the "long shot" ATS.
Generally speaking, it's usually a good idea to bypass HR (and their filtering systems) for the early stages of your communication with the potential employer. This is not always possible, sometimes you just have to use the ATS and leave your resume to fate.