For CSS Profile schools the difference between NPC inputs (assuming it’s accurate) and FAFSA are likely dramatic. Some things that Profile will include that FAFSA doesn’t: non-custodial parent income/assets (plus their new spouse if there is one), current home equity (market value less debt) and investment property/farmland.
FAFSA is primarily used to qualify for Federal Financial Aid. Some FAFSA only schools may use it to disburse institutional aid, but AFAIK there are no FAFSA only schools that meet full need.