It will make a difference in computerized rankings used by the CFP Committee given half of the SEC teams will now be guaranteed an extra conference loss. The ACC needs to do likewise.
The SEC (and ACC) playing another conference game levels the playing field with the Big10 & Big 12.
But I have a feeling the SEC is smart enough to make sure that extra game for the top 4-5 SEC schools in preseason rankings will be played against schools with preseason expectations to finish 10-16 in the SEC.
With 16 playoff teams there will definitely be 3 loss teams and I'd bet there are some years 4 loss teams get playoff bids. So that minimizes the risk of SEC & ACC schools adding a 9th conference game.
IMO what might be more important with a 16 game playoff is more non-conference games between P4 schools so their is a larger sample size of inter-conference games. Currently, Iowa States schedule is pretty typical with: 9 conference games, 1 non-con P4 game (Iowa) and 2 G5 or FCS games. In the future, maybe schedules need to be: 9 conference games, 2 non-con P4 games and 1 G5 or FCS game. Coaches wouldn't like it, but TV partners & Fans would.