Boxes 1 & 3 (and 5 too) will not necessarily have the same figures. Most commonly, you'll see Box 3 greater than Box 1, which is -- as you thought -- a result of subtracting pre-tax items such as retirement plan deferrals.
But Box 1 can also be greater than Box 3, since Box 3 (social security wages) is capped at $118,500 of income (for 2016). After that, no additional social security tax is withheld. Box 5 (medicare wages) is not capped.
