Contagem de tempo was never an obligatory document for citizenship application. Some people believe that it could help but we do not have any proofs that it really helps. AIMA asks IRN if the applicant fulfills the residency requirement at some point in the process (estimation 6-18 months)
However, if there is doubt about the starting date it is recommended to get contagem de tempo and to see what AIMA writes in it before applying. Takes 2 months and 40 euros.
As for expired card during the process, in the past, AIMA did not take the covid prolongation into account and replied “does not meet the requirements” if the card was not renewed. There are some indication that it possibly will accept covid prolongation now. However, it is not tested yet by anybody. On the other hand, I am not sure how long they could cover themselves with this flimsy covid prolongation as covid measures are gone for a long time. I expect them to stop this practice sooner or later. Maybe another half a year? Till this year end.
Contagem de tempo could not be used for PR not only because AIMA, having all info, does not need it, but also because contagem de tempo itself says “for the purpose of citizenship” The changes in the law were only about citizenship, so yes, we have an absurd situation when right for citizenship may happen earlier than right for PR.