Can I stay in Schengen more than 90/180?

Since you are applying for citizenship of Portugal under the terms of the Golden Visa program, you have presumably held such a visa for at least six years. If that is the case, then you are a Portuguese resident, and time spent in Portugal does not count for the 90/180 rule. In that case, you can travel to France without any problem.

If in fact you are applying for the golden visa for the first time, you are exempted from the 90/180 rule in Portugal while this application is pending, but time spent in Portugal still counts as far as authorities of other Schengen countries are concerned. In that case, you would not be allowed to travel to France after spending 90 days in Portugal.

In practice, however, you are unlikely to encounter any problems if you travel to France, since there are no border checks unless you drive through Andorra.

Since you are apparently not a Portuguese citizen at the moment, the answer would seem to be negative. France grants extensive rights to EU citizens but is not bound to recognize any special status or tolerance granted by Portugal. So waiting for Portuguese citizenship is not relevant per se.

In practice, there are a few details (including the lack of border controls between France, Spain and Portugal) that makes the situation a bit more blurry but as far as the letter of the law is concerned and until you actually become a Portuguese/EU citizen, you have no right to be in France past 90 days in the Schengen area without a French long-stay visa or residence permit.

Alternatively, a Portuguese long-stay visa or residence permit would also work in this situation because the time spent in Portugal would not count towards the 90-day limit and only the stay in France would happen under short-stay rules (cf. Can I visit Schengen countries on a Type-D Schengen Visa?).