Has anyone found a native way to automatically send order confirmations to a customer after a sales order is saved? As well as invoices once genereated? We know Cloud Coders is an option but looking for a native way that does not require external bundles.

You can do it fairly simply using workflows that just need to be dependent upon the document type being saved and/or created

Could mark the SO/ invoice for email, so the PDF serves as a confirmation. To automate, set To Email on the customer record > preference

And this program will send an email on our behalf? Who will the email come from?

It depends how you structure it. If you use the default functionality of emailing all documents for the customer then it would come from the user who created the document. If you needed a more nuanced solution then the workflow has a number of options for the sender (hard-coded, user who created, some other user). I'm working on a similar project for a client of mine and have done this many times before but it really does depend how nuanced the emailing situation needs to be as how to best accomplish it. Feel free to DM me is you want to discuss further

This scenario can be handled with saved searches, scripting and email templates that get triggered automatically - Feel free to message me if you are needing any help