Honda, like many manufacturers, are going "Green" and this means an attempt to minimize waste. Early oil changes are considered as extra waste, hence they recommend you leave the oil in and change it at the regular interval.
I personally believe an engine is done with break-in after 1-3k miles (if done right, you should have put the engine through its paces after that many miles (many hot / cold cycles, wide open throttle pulls, highway cruising, etc, etc) and its a good time to get the oil that's now full of metallic shavings outta the engine.
Of course we all know that the block will be perfectly fine even if you leave the oil in place for the full maintenance cycle but many still dump it because its technically healthier for the engine.
Just my opinion.
I also agree on running the Honda synthetic blend oil for the second oil fill before going to synthetic on the second oil change (after 10k miles or so)