You way involves the employer making a deduction from each paycheck and then making an ACH payment for each employee to the institution of the employee's choosing. For a large company that is thousands of additional transfers. The way a company like Gusto could maybe do this is to store an employee's IRA account information like they do their bank information for direct deposit.
Also, FYI, when buying mutual funds through your 401(k) you aren't charged any fees for trading. Through my IRAs at least I get charged a commission for every purchase. With payroll deductions those would add up.