People CAN file cases and documents on federal cases, through USPS mail or other courier services, etc.
Only pro se litigants can file paper in Federal Courts. Since there are no pro se parties in Trump's case, the clerk had no business filing a paper copy of a motion received in the mail. See the portion of the Local Rules for the Southern District of Florida, below. If an attorney wants to file non-ECF, that is mail in some paper to be filed, they first need to request permission from the judge assigned to the case. All Federal Courts have been electronic courts since 2006, and some, like the ones I practice in have been electronic for at least a decade before that.
"2A. Electronic Filing Requirements On October 12, 2006, the Southern District of Florida implemented CM/ECF, an electronic filing system designated for use nationwide by the United States Courts. Electronic filing is mandatory for all attorneys admitted to practice in the Southern District of Florida. For additional information, refer to the CM/ECF Administrative Procedures. United States District Court General Civil Case Filing Requirements Southern District of Florida 2B. Pro Se Litigants Pro se litigants, or individuals who represent themselves, are not permitted to file electronically. Non-prisoner pro se litigants may receive notices electronically after filing the form “Consent by Pro Se Litigants (Non-Prisoner) to Receive Notice of Electronic Filing” which can be found on the Court’s website (www.flsd.uscourts.gov). For additional information, refer to the CM/ECF Administrative Procedures. See Attachment A (Sample Document)."