To be fair there are surprisingly few Intel motherboards that support 3-way SLI (I'm less familiar with AMD boards), where each slot has a
minimum of x8 lanes, as nVidia demands for it to be officially supported; with Intel you're limited to an LGA 2011 board or an 1150 board with a PLX chip.
Of the LGA 2011 boards that can run 3-way, but
not 4-way SLI, the majority if them only have 6 expansion slots, so they can't run a 1-4-7 setup, and instead run 1-4-6.
Of the LGA2011 boards that can run 3-way, and can
also run 4-way SLI, the needs of 4-way SLI dictate having x16 slots at the 1-3-5-7 positions. It's rare, but there are boards that have an additional slot at the 4 position, for example the
EVGA X79 Dark, which providing you don't have anything in the x4 slot, should run 3-way SLI in slots 1-4-7.
When it comes to the LGA 1150 boards that feature a PLX chip, that effectively increases the number of PCI-e lanes available for graphics cards, the same thing happens as with the LGA 2011 boards; being able to support a 4-way SLI setup, they have to have x16 slots in the 1-3-5-7 positions.
With the LGA 1150 boards with a PLX chip, the PLX is an expensive component, so while they could produce a motherboard with one that only supports 3-way SLI (in the 1-4-7 positions), I assume they must consider the potential market for one to be small, when you could get a similar board at a similar price that supports 4-way SLI.
I guess it all comes down to a combination of necessity when designing the boards, and the limited potential market for boards with the ideal 3 card setup (keep in mind the number of people running 3 card setups is very small indeed).