Augment runes and the higher stat food are there for min-maxers that want to squeeze every bit of potential out of the system.
There is also an economic side to this, with raiders selling BoE items from raids and using the profit to finance consumables and repairs.
Augment runes allows the team to have a baseline solid reward from Raid Finder when you don't win an item.
Past expansions gave you 28 gold, which didn't make anyone feel good.
The augment runes can actually sell for a decent amount early on in the expansion, which is a better solution than dropping hundreds of gold and causing inflation.
The intent is for augment runes to be a nice bonus to players in Raid Finder, not for Mythic raiders to feel that it is necessary to run Raid Finder.