Does anyone know if using Championify qualifies as a 3rd party program?

As far as I'm aware, the application doesn't violate the Terms of Use, as it doesn't interfere with the game once the match has started. It's essentially the same thing as transferring another summoner's item set file to your computer.

Not to mention, various Rioters use this application.

it's totally kosher. it fits well within our policies, and we even released some clearer documentation on item sets to make doing this stuff easier!

If it isn't a Riot branded program, it's 3rd party, so use at your own risk.