Ok, so as of this month, currently, autofills and 1/3/5 cafs actually have the same triggers. For those who didn't notice, autofills are smaller and cafs are bigger now. So if an early morning autofill rolls, then the whole thing will roll into a CAF. Unless it is ACCS, BBO2, BOYS, GIRL, JLRY, MENS, SHO1, SHO2, or WMNS, which never pull in the cafs - those would roll into the next days autofills. They wouldn't necessarily be huge if other receipts or batch fills filled those fillgroups in the inbetween times.
Not pulling CAFs within 2 hours will affect your CAF pull timeliness, which shows up on the main page for logistics my performance scores.
Not pulling an autofill before it rolls will turn one of the metrics on the freight flow index yellow: the pull metric. Anything less than 100% is considered at least yellow. I think 95% or less is red.