Most companies around these parts use similar services for resume intake, and those that don't seem to use email.
For the former, I haven't seen a resume handling service that doesn't have a "Cover Letter" text field, so if we can stipulate that those are common enough, why would an applicant leave it blank?
For the email case, it's a bit cold and impersonal to send an email with a resume attachment or URL with only whatever few words are necessary to keep your email client from popping up a warning questioning whether you really want to send an empty email.
* Because it generally goes to /dev/null. Possibly literally.
* Because the time you need to get a cover letter ready and uploaded, the fucking session has expired and you need to restart the whole fucking process. Again.
I do write and send cover letters, and I hate all the online application systems with all my heart. It's awfully time consuming, nerve consuming (those web forms always suck donkey balls, the required fields are cryptic, and you need to re-type in a gazillion fields what you have already typeset in the CV you'll be required to attach anyway) and you (well, I) never get any answer past the automatic acknowledgement that I sent an application.
I am fine with any requirements for the interview process as long as they are clearly defined.
You're describing what worked for you. You don't know what works for other companies that are hiring.
You don't know the percentage of companies that look for the same things you do, the percentage that use an automated resume filter that simply ignores cover letters, the percentage that do something entirely weird and unexpected, the percentage that believe the cover letter is much less relevant than an active Github profile - and so on.
I wish employers would stop making this basic mistake. If you want a cover email, ask for one. Don't assume that you have an industry-standard application process (you don't - no one does), that applicants who don't match your unspoken requirements are bad (they may or may not be - you have no more information than anyone else does), that your special hiring process quirk gives you a deeper insight into applicant quality than any of the tens of other possible hiring quirks (it doesn't), or that your company is special enough to ignore all of the above (it isn't.)
If you want to articulate that you're looking for personalities with enhanced conscientiousness as an explicit hiring goal, that's one thing, especially if you're willing to trade off other qualities in the Big Five.
But randomly picking an action and assuming it gives you hire/fire information with no further context doesn't seem usefully rigorous.