All customer communications done through QuickBooks are currently sent to the main email address, kfitz.
Although, the Alt email address are automatically copied when invoices and other sales forms are sent. You'll also want to follow these steps if you want to check if the invoice was already sent or not:
We'll send a feature request about the sample scenarios that you've shared with us here to our engineers. They are collecting feedback and suggestions to reviewed in the future updates.
Don't hesitate to tap on us again or post a separate question if you need anything else.