Scholars actually
pay journals to publish their papers. No, this isn't vanity press or a bribe. Scholars must work very hard to reach the point where they can pay those fees.
For example, say you submit a paper to Nature. Odds are it will be rejected, because Nature has a high impact factor. Say your paper is both accepted and passes the review process. Now you have to pay Nature to publish your paper. Depending on the options you ask for (e.g. making it free to download costs extra) you can wind up paying thousands.
No university is going to say to one of their researchers, "Hey, could you maybe not get accepted by Nature quite so much? It's expensive!". Nature knows this.
Also, the format of submission varies by field. While word files may be standard in some fields, in others latex is expected. Obviously, typesetting a latex document is pretty gosh-darned easy for a script to do.