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We have a legal requirement to, for every invoice, include an identifier issued by tax office (an UUID).
From what i understand options are:
Note - doesnt really work since its global and not invoice by invoice basis
Custom Fields - these could work but are defined on entity level (subscription, customer...)
Customer Invoice Notes - again set for all invoices for this customer
Both Customer Invoice Notes and Custom fields could be worked around by updating them just before sending out the invoice but im assuming these would need to be updated just before generating the invoice which is not our case since we use metered billing (invoice gets generated on the first, during the month we collect usage and apply it, fetch the UUID from tax office and "apply' it to invoice before collecting)
We have had a lot of requests from certain EU based prospects requesting us for a logic to display a unique identifier other than the invoice number. This is currently not supported but we are currently analyzing it due to the legal nature of it.
Unfortunately, I cannot commit on an ETA at this point in time but as you yourself mentioned, you can use a custom field and populate it with the UUID before the invoice gets generated.
For the first invoice, you can simply void and regenerate it such that the UUID gets displayed on the invoice.
You could do this by creating an invoice note at the subscription level. This can be done by navigating to Subscriptions > Select the subscription > Add Invoice Note. By doing this, the particular subscription's invoice will have a separate note and it will not be available on the other subscription invoices.
Alternatively, you could create a custom field note for the invoice but as you said, you will have to apply it before the invoice is generated. Unfortunately, we do not have any other way of supporting this requirement. However, we do have plans to implement this in the future.
Hope this helps. Please get back to us for any further queries.