Hi,
About the second point (HikaSerial), the confirmation email that you can send while changing the status in the backend could not contains serial if the previous status is not compatible.
For HikaSerial, the email content is based on the current order, so if there is not serials attached, it can displayed it.
When you validate the popup, the order status would change and HikaSerial would attach/assign serials.
So, I can recommend you to use "two step".
First : change the order to a compatible status without sending an email - HikaSerial would attach serials.
Second : change the order to the final status with the email - The email content would be right.
About the first point (Attached Invoice), I think that the plugin requires a little update.
I think the plugin would not generate the invoice if the price is zero. Maybe an option would be a good solution.
Regards,