I would wait until you hear from them, unless it takes a lot longer. The atestado shouldn’t be relevant as long as your tax address was changed in the system in 2024.
Have you verified that you’re able to issue a residence certificate from within Portal das Finanças?
You can do that by going to this page, then selecting Domicílio Fiscal from the drop-down, followed by Confirmar.
Yes, it’s there
Just confirming - is NHR 1.0 gone for good? No way to apply now as a golden visa application who is not a resident yet?
Did you gain PT residency for tax purposes (not necessarily the same as actual residency) by 2024-12-31 ? If yes then you have until the end of next month (March) to request old NHR.
Assuming the GV application was submitted before 31st December 2023. Or commitment on a lease, job etc in PT by a similar date in 2023.
I submitted my application for NHR and have been asked by the AT to submit proof that I was not resident in PT for the years 2019-2023. What would be acceptable proof to submit?
You’d think they could check their own system… 
Perhaps provide proof of where you did live, and pay tax, during that period
I’m requesting an IRS certification, but god only knows how long that will take. Also getting property tax statements from local county and some utility company statements. See what sticks