What you send as you apply for a job will vary, but the overriding rule is “Follow all directions exactly.” When the job ad says, “Please send a cover letter and résumé in Word format to...,” then by golly you send a cover letter and résumé in Word format. Don’t substitute a PDF for Word or put it all in plain text because you think that’s what makes more sense. The company specified Word for a reason, and their reason trumps any you might have.
If the ad doesn’t specify how you should apply, assume this:
You’ll send a cover letter in a plain-text email, with the name of the position in the Subject field.
Your résumé attached to the email as a file attachment in either Microsoft Word or PDF format, with your name ...