RC transmitters for drones with a programmable flight controller

My questions are basically about this:
Since you can have a programmable flight controller (APM, NAZA, Pixelhawk, etc.), and you also get very good RC transmitters with programmable features, which is more important when it comes to setting up?

I’m an old (in more ways than one, heh) RC plane pilot, where I did all my settings and mixing via the transmitter. But with a drone flight controller, seems a lot of functions are now available on the controller settings.

I’m also well knowledgeable with micro processor programming, Having played with PIC’s, Atmel, Arduino and Raspberry over the years. This is exciting to me, to be able to use and play with this knowledge with drones.

So, which is more important? RC TX or flight controller?

I’m in the market for a transmitter now, and I don’t want to spend much money on something that can be duplicated on the flight controller and have features I will never use.

Suggestions for a good RC TX would be welcome though.

Answering my own question:
This series of videos are very helpful:

Especially video 3, which discuss TX setup.