it evens out.... if you win the SEC champ game and win, you get a bye week in the playoff and 2 win two more tough games for the championship. If you are not in the SEC champ game, you have to win 3 tough games in a row for a championship.
Each scenario has it's benefits. Winning the SEC gives you a good break to a two game playoff. Not playing in the SEC gives a longer time at the end of the season to heal up and get ready for the 3 game playoff.
Each has it's cons. Winning the SEC requires beating a quality team at the end of the year where you might already be beat up. Winning the National championship with out the SEC championship will require a 3 game win stretch of quality teams.
I think it really comes down to how healthy you are at years end as to what is best for your team. If you are healthy, an SEC championship game is desired as it breaks up the 3 game stretch. 1 hard game for the SEC champ, 2 for the national championship later. If you are banged up at years end it may be beneficial to have the time to rest and recover and then hit it for a 3 game NC stretch.
The other possibility is you play in the SEC champ game and lose and still make the playoff. It would be good to still be in the playoff, but now you're playing 1 extra game on the season which makes it much harder.