It's so that drivers would see the cyclists in junctions. If the bike path is separated until the junction, it's common that drivers don't pay attention at all to what happens on bike paths and turn right into crossing bike traffic. What makes things worse is that usually there are bushes, placards, bus stops and others between road and bike path, all of which block visibility and grab attention.
I like your optimism. I've heard that in the Netherlands, the solve this problem by having a red turning arrow when people (on foot, on bike or in cars) are allowed to go forward. So in drive-on-the-left terms, vehicle traffic is allowed to go from the south to the north or east or from the east to the south. Since people who are driving cars from the south and want to turn to the west are obliged to stop, there's no possibility they'll unintentionally charge into people walking or riding bikes across the western entrance. The disadvantage is it requires four cycles not two, and therefore reduces the time pedestrians can cross.
On Albert St and Swanston St in (East) Melbourne, the separated lane stops at intersections so that cars can use the bike lane to turn left. People riding bikes are supposed to give way to people driving cars and then filter around the stopped cars into the bike box ahead of the cars. I never really feel safe using the Albert St lane for this and other reasons. Fortunately I have other options.
