Firstly, early filing is 90 days, not 3 months. 3 months can be less than or more than 90 days which makes it wrong to use.
Secondly, no, early filing does not apply to filing under 4 year and 1 day rule. You're already filing early instead of waiting 5 full years.
This calculator doesn't account for 4 years and 1 day rule AFAIK.