You could, however if a button was mapped to Flirc and the function on the tv setting you were using then it would cause both to react.
You set "channel up" button on your remote to Stop button in Flirc (for a media app) - this would cause the channel to change and Flirc to stop the video the media box was controlling.
An optimal situation for Flirc would be to use a remote that would be used at the same time (e.g. a DVD remote - if you used it to control a media centre and a DVD player it is unlikely you would have both machines on at the same time)
A multi-remote such as the logitech harmony remote (or most other remotes)