One reason you can't bring young kids through the line is that many (not all, but many) load stations are simply far too fast-paced to have to worry about measuring every kid comes through the line. Try having to load 34 people onto a train in 54 seconds, but then also having to leave your position to take every 5th or 6th child to be measured at a height stick 20 feet behind you (not all height sticks are in convenient locations once you get to the station). That's why the measure them out front, to weed out most of the littles, and the ones in the station are for a few that somehow sneak through (whether intentionally or accidentally). Also, many stations are not big enough to accommodate the dozens of families doing a child swap at any give moment (BTMR, Splash, Kali, are a few that come to mind), or in some cases you don't unload in the same place where you load (Everest, R'n'R, etc). It'd be a great idea in theory, but Disney's queues and loading stations simply aren't built that way.
