Yeah, I thought about xpubs too but like you said; it’s the accounting coordination that causes complexity. This is already fairly easy with lightning, but Bolt12 on lightning will make this a lot easier.
An xpub is all that is needed for payments on the chain. You can export hundreds of address upfront, and so you have your basic raw API at hand in a text file.
The problem is integrating it smoothly with the user billing system. Perhaps you can use something like https://books.libreoffice.org/en/WG71/WG7114-MailMerge.html for a basic automation (but you miss the qrcode goodie).
For LN you can use some service like LNbits, I suppose there are several that expose an API, along with a GUI for the invoicing system.
Discussion
Yeah, accounting frictions :/