IIRC from what our lawyer said years ago, the citizenship application is submitted based on a document of proof of legal residence requested from SEF (now AIMA) which mentions the start date of legal residence. I think it’s the Certidão de Contagem do Tempo. Not your entire dossier of stays documented with NIFs and air tickets. That appears to have been checked only in the previous offline renewal process which required fresh biometrics and documentation. I think the current nationality process assumes that if you have a valid card at the time of application and the Certidao mentions a start date > 5 years before the application date, you must have legally resided for > 5 years.
(This does appear too good to be true, but then online renewal of GV without any documentation was also too good to be true and it did turn out OK)
@Mr.E can hopefully corroborate with more details: Path to citizenship after 5 years on GV - #19 by Mr.E