internal pullup resistors & digitalWrite

It kind of mirrors pin 13 with the flashing LED - you can just plug an LED in without worrying about resistors.

Yes you can do that to make things simpler for beginners, but its not good practice. The current Arduino boards do not have a resistor in series with pin 13 (its only in series with the internal LED) so the typical red LED plugged in directly will exceed the Atmel recommended pin current.

That, and starting off with external pull-downs are the way many people have been introduced to Arduino, but they are not necessarily the best way to learn.