AVR Freaks

You don’t need an arduino board. The Arduino uno has a mega328. You don’t need to bootloader - that is for convenience. You can use the Arduino tools to build your code and generate a hex file. As for ‘limitations’, that’s most likely comments from an uninformed person.
So, to reach your goal, just load the Arduino tools, select uno for the board and build the example code for manchester. Burn the hex file into your mega328. Job done. Verify the operation then make your own mods.
Arduino uses avr-gcc, so whatever works for that will work with Arduino.

with intention of implementing it to a following robot later on.

Small world.

As luck would have it I happen to suddenly have found myself doing the hardware for a simple line following robot based on an Arduino Nano board, and a cheap chassis from the web.  Another individual will be working on the software to make it run.  It is for a school competition.  

The rules say the bot can upload data for analysis, but must run autonomously, i.e., it can't receive any guidance from a separate computer.

The exception is a simple On/Off - Start/Stop RF link, if desired.  One can turn the bot on, set it on the line, and then use the RF link to turn the bot on.

I wanted to keep this project simple, software wise, so I elected not to use the little cheap 433 RF modules.

I've used them before, very successfully, without Manchester encoding, but I used short data packets, warm up characters, a start of packet character, the data load, and a check sum to make them work.

For this current project I ordered the cheap Bot chassis from Banggood Electronics, and they also had a cheap Key Fob RF remote, with 4 push buttons, for $3 or $4 each.  The receiver has a data good signal, and four data output pins to indicate which button was pressed.  Trivial to implement, cheap, and certainly less software intensive than writing one's own Manchester encode/decode routines, or even the packet parser for the above alternative option.

Good luck with your bot!

JC 

Edit:

Breadboard with the Prototype, two LEDs simulating the motors.

The RF Key Fob showed up yesterday!

JC

To use the Arduino system you need to download and install the Arduino IDE on your PC.   The IDE [integrated development environment] has all the background files needed, such as pins_arduino.h.

But the problem isn't using Arduino: it's using junk libraries from GitHub.  Junk libraries are those that don't have enough documentation or low-level example programs so that people how don't have PhDs in Atmel AVR can get really simple demo programs working without having to read and master a 300-page professional engineering IC data sheet or calling on their 10-years of engineering level experience with complex computer compilers.

The code shows nothing more than a pin toggling at 1Hz.  There is a main() function, which means that the code is not in Arduino format, which would be using setup() and  loop() functions instead of main().  However the downloaded libraries are written for Arduino.

I suggest that you abandon using Atmel Studio and use the Arduino IDE only.  Buy two Arduino Nano module boards from eBay/aliBaba for $6 and then download any code that you can find for using the FS100A to transmit tiny amounts of data small distances (30-300cm).   Manchester encoding is for semi-reliable transmission/reception of lots of error-free code packets using flaky simple radio-control systems.  You only need to send one bit every half second.  You don't need the hassle of Manchester encoding or Atmel Studio.