A three team rule seems directly targeted at the SEC, but might not work that way in reality, if it happened. I lean to thinking it wouldn't happen. My GUESS is they'd include the best G5 team in the playoff as a semi-pastry for the one seed. That would leave only two slots for at larges, and it would be very rare indeed that both would be from the same conference, rare enough not to worry about it.
Would that have occurred any time in the past 20 years, possibly? When UGA and Bama both made the top four, Auburn might have slid in to 8. Maybe. They had three losses, probably not. I think you'd need two 12-0 teams in the CG and one very good looking 11-1 team AL when nobody else was that good.