Flashing NodeMCU with .ino file?
Last question first: The ESP8266 is the main IC on the NodeMCU board.

This is similar to the idea that an ATMega328 is the IC on Arduino Uno.

A normal 'clean' Arduino IDE install can work with an Uno ('flash with an INO'), but not with an ESP8266 based board. For this, you will need the ESP8266 addon for the Arduino IDE, after which, the NodeMCU board is available as an option.

This page documents the ESP8266 addon:
https://github.com/esp8266/Arduino

Long story short, open preferences (File -> Preferences) , under Additional Board Manager URLs, add http://arduino.esp8266.com/stable/package_esp8266com_index.json

Click on Tools>Board>Board Manager (assuming you have Arduino IDE 1.6.4 or later) and search for ESP8266 and install the option that includes NodeMCU.