Why mate two boards instead of using one thicker board?
It has to do more with the quality of the the 2x6s vs the 4x6.  A 4x6 x 12 board would have to be clear all the way through, with no cracks or knots. Most softwood logs won't produce this board, and if it cracks, it is likely to break more easily vs the 2x6.

On the other hand, drilling a bunch of holes in a 2x6 does it no favors, though because the two boards are tied together, weak spots in one board are often compensated by its partner.

So, if you could find a really good 4x6, go with it, but otherwise use the 2x6.  In most cases, the 4x6 will be more expensive due to its rarity.

In colonial times, they would have gone with the 4x6, as they had lots of hardwood timber and each individual cut took a long time.