Endcaps add length to the entire tank. It depends on which brand endcaps you use. However, most canopies/hoods are built wider than the tank as well (they have to be to some degree to fit over the top of it). I've usually designed a hood with a couple of extra inches in it, but staggering bulbs is certainly one way to handle it.
Or just get MH bulbs and save yourself lots of trouble down the road.