There is no seeding when it's done that way. As such, your top 16 are unlikely to actually be your top 16 since somewhere along the way they will get eliminated from other folks.
In large events, you'll do ~4 rounds of swiss to "figure out seeding" and then cut to top 16 or whatever and then do single elimination. But when you're running <16, a cut to the top 4 doesn't really mean much.
I will say that I have issues with swiss style pairing in addition to FFG's tie breaking system. All too often it seems like the top two players meet at the final table (in the case of 16 players and 4 rounds... going into the final round there's only 2 people 3-0... winner takes 1st. But common sense to me seems like the loser should take 2nd. But all too often, one of the folks that was 2-1 ends up 3-1 and either via SoS or modified wins ends up taking 2nd place. And whomever lost at the "final table" comes in 3rd or 4th or something like that.