An employee can convert a $1000 increase into a $1000 MIRI donation, but that requires the employee to get up and do something (i.e. log into his bank account and do a transfer). There's a chance for procrastination, laziness, and mental inertia to prevent that donation; employees who really want MIRI to get the donation might appreciate the company handling the actual getting up and doing it part (which the company can do rather more efficiently - making one big transfer instead of hundreds of little ones, with a corresponding decrease in both individual effort and bank fees).

Also, since we're talking potential employees, then it might be a strategic move by the company to more strongly attract potential employees who strongly value MIRI donations and reduce the company's attraction to potential employees who do not value MIRI donations.