You are mixing up pull-up/down resistors (which ARE on the board) with current limiting resistors. (which are NOT on the board).
There are also pull-ups on RX and TX on the pcb I believe. These prevent noise on those pins confusingthe bootloader at power up.
Ok, correction:You are mixing up pullup/down resistors (pullups ARE on the chip, which is on the board) with current limiting resistors. (which are NOT on the board, except in the circuits that contain LEDs of course).
Strictly speaking you are right. But resistor is still resistor: internal "pull-up resistors" may be used as current limiting resistors to power LEDs/transistor bases or any other light load.
This is wrong: "internal "pull-up resistors" may be used as current limiting resistors to power LEDs/transistor bases or any other light load." All the internal pullups will do is very weakly light an LED if the pin is set to an input and the LED Anode is connected to the pin and the cathode to Gnd. If the pin is set to an Output and there is no external current limit resistor, the IO pin or the LED will be damaged eventually. And maybe sooner rather than later.
It is possible to activate internal pull-up resistors on Arduino. It is as if you connected 20-50k resistor between 5V and the pin. This way you may drive LEDs without other resistor. But depending on your expectations and LED you use it may be too dim. Also it is a bit dangerous - if you configure the pin as OUTPUT HIGH by mistake, you may damage the LED and/or Arduino.
1. Use a resistor with a LED, that is, don't depend on the internal pullup resistor.2. The point of the tutorial Example 02.DIGITAL - DigitalInputPullup is how to use the internal resistor to prevent the switch from floating. I am trying my best to leave it at that, although I have as many questions revolving around the topic for several posts.