Note: For Romania, Bulgaria and Cyprus the basic Schengen rules apply
- other than that the 90 days period is seperate from the other areas
The 90 days in any 180-day period rule is a seperate condition that also applies to most nationalities that don't require a visa.
For a visa holder, the duration of stay field of the visa sticker should contain 90 days. Any number that is less than 90 means that the duration of that amount days must not be exceeded.
Both (visa and non-visa nationalities) can be refused entry if the 90 day condition is not fulfilled.
When you apply for a visa, you must give an itinerary, which will include an entry date.
When you make a visa application, they will check the previous visits to ensure that the itinerary is possible.
They would either suggest another period or reject the application if the 90 day condition is not fulfilled based on the planned itinerary.
Is it fine to apply for it before 91 days have passed since my absence?
If that is the case, what happens if I am granted the visa before 91 days pass?
You can only use the visa when the 90 day condition is again possible.