IMO this is like asking piano vs guitar. Depends where your skill set is. Both have advantages and drawbacks but the actual difference in real life scenarios would probably be small enough to be a statistical equality (in the right hands).
Someone who is great at KM will be better than someone that is average with a joystick, and vice versa.
As long as your setup doesn't stop you from doing something, you should be fine.
When I started with E: D, I used an old joystick plus my keyboard. Once I learned the binds, I was able to do pretty much anything in terms of moves.
Then I switched my joystick for another model and got a throttle and was horrid but after a while, got used to it and could do as much as before, just more comfortably
Then added rudder pedals, and had to basically relearn to fly a bit, but now I'm confident again in my abilities.
It's just a matter of time with the tools you have and in the end, what type of experience you are looking for.
Just out of interest why would you need three axis on a throttle?
Isn't throttle just forward or back?
I have a throttle, might give it a go. I also have track IR but never used it for flying in Elite.
The CH pro throttle has the main axis, plus a thumb joystick that can easily be used for such things as vertical and lateral thrust.