Electronic – Analog and digital input pins

Yes, the analog pins on the Arduino can be used as digital outputs.

This is documented in the Arduino input pins documentation, in the Pin Mapping section:

Pin mapping
The analog pins can be used identically to the digital pins, using the aliases A0 (for analog input 0), A1, etc. For example, the code would look like this to set analog pin 0 to an output, and to set it HIGH:
pinMode(A0, OUTPUT);
digitalWrite(A0, HIGH);

By isolated, they really mean a supply isolated from the switching noise of the rest of the circuitry.

When digital circuitry switches low/high or high/low, a sharp current is drawn during the transition of many totem-pole logic drivers within the ICs. This creates noise on the supply rails, which local decoupling capacitors try to reduce.

The performance of the PLLs is reduced by such supply noise so they benefit from a cleaner supply rails. The LC filter does this. The inductor blocks conduction of the higher frequency noise while letting the DC supply through. The capacitor smooths the supply and acts like a local rechargeable battery, providing current as the PLL switches as the inductor will block the transient current flow into the PLL. (This is basic LC filter in DC supplies stuff so you'll find plenty of decent text on the interweb about it.)