I'm not much of a botanist but I have to ask: with so many different varieties of magnolias, which one is yours? Is it the evergreen or deciduous type? They don't usually need a lot of pruning unless you're trying to make them fit into a smaller space. But some varieties have a tendency of sending strong vertical growth from the bases of the main branches and if that's low enough, they can become a secondary leader trunk. It's not really good for the tree and may eventually lead to splitting the tree in a strong wind. Since they can become really large and imposing trees, they could do quite a bit of damage coming down. You might want to prune such shoots early on.
But I would think a 5 y.o. tree has already passed the age where this is of much concern though. At this age all the pruning is going to be done for shape forming and so I don't think there would be any special concern for the lower branches. This is where it gets to be more aesthetics and I hope some of our visitors more familiar with that aspect of gardening will chime in here.