It's not inconsequential. Timing plays means that a second off due to a penalty leads to an incompletion, or not enough YAC. Even dump offs, anything can happen, see Ray Rice on 4th and 30.
Any penalty that disrupts an offensive player should be an automatic first down. And while it's rare for someone to take a penalty on purpose, I think it's also rare that 3rd and 20s get converted because of a penalty. Sure, it happens, but it's not a plague on the game.