There are three types of risk being avoided here. The first is the most obvious and blatant check fraud. Because the law requires policies to be applied uniformly, then exceptions have to have policies as well. In other words, if Policy A does not work for customer X, then customer X has to qualify under a broad exceptions rule to make Policy B available to them. It simply costs less to mass deposit online than to have a person walk in the door, place themselves on camera and in the same police jurisdiction as the bank and commit fraud in person. Blanket policies have no marginal cost in this case.
The second is money laundering. Any large deposits could potentially trigger a money laundering investigation. Having a person deposit the funds in a branch gives the bank or other financial institution a chance to "benignly" interrogate the customer.
The third is kiting. Even a financial institution has been caught kiting before. Some elements of the check clearing system are quite dated. The US is decades behind other parts of the world. You can still do kiting in the US and get away with it. Nonetheless, kiting is a crime and it is one a bank is responsible to detect. Kiting becomes easier if you can deposit electronically.
Accepting deposits create liabilities and placing a physical limit on deposits reduces them. A physical check can have fingerprints on it, an electronic check cannot. An in-person deposit requires a person to go on camera, an electronic deposit could even happen in the International Space Station.
The risks for long-term customers is incredibly low. That said, there are plenty of fraud cases of good firms that had a sudden change in management or accounting that suddenly became a bad risk. Blanket policies are the problem and the inability to underwrite individual firms and people. Of course, the fees would have to go way up if they were to allow all potential customers to undergo individual underwriting.