I always record DI and Amp'd guitar tracks as a stereo file, DI on the left and Amp on the right. Then I use this JS plugin I wrote to choose which side is being used. That way the recordings always stay "grouped" since they are the same physical stereo file ;) It's basically exactly like your FR, except instead of having 4 takes for two performances you only have 2, and you just choose whether the DI or Amp is being used based on the output configuration set up. The first recording input being the left input and the secondary being the right ;) Multichannel media is definitely the most logical way to handle permanently grouped sources IMO!