Not necessarily. We use an online application system and yet every resume is reviewed by a person. Part of the reason a lot of companies do electronic submittals is not to remove the human touch, but to remove the human error and bias. If every single candidate is received electronically, there will be a trail. People can't 'accidentally' misplace resumes of people they don't like for one reason or another.
Anyway, you can add a cover letter with additional details that are not in your resume. Just address it to "Recruiter" or "Whom it may concern". A Word or PDF letter format is generally the best and you can usually attach it to your profile/submittal.
I wouldn't worry about references or a transcript unless you were a recent graduate with no work experience (or unless the posting specifically asks for it).
It is a good idea to tailor your resume to the job you are applying for but I wouldn't make it too specific because a lot of times, someone may not like you for *that* job but may have other openings that might be a better fit. That would probably depend on how just how large the company of interest is...
Good luck!




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