It doesn't really save them money, it just means they can report that number and get a public pat on the back. I highly doubt they were planning on donating that money w/o customer donations, they likely looked at past donations and figured this was a safe number to go for.

Donating through one of those prompts doesn't help or hurt the company in any meaningful way, other than allowing the company to take credit for your donation (not on taxes, just on public statements).