The print setup is used to help QBO align the amount on the check, sweetchef-scalia.
Being able to customize the font used on the checks sounds awesome. I'd encourage you to send this idea to our developers. We update QuickBooks Online a lot, and there might be a chance to have this option added soon. You can visit our feedback site to share your thoughts and suggestions about the program: https://feedback.qbo.intuit.com/.
I'm always here if you need anything else.