It's an obvious form of comparison, like putting two different bookshelf speakers on L/R channels. But you will want to compare pairs for your final evaluation. I would never use this method as my final determinant of sound quality and would not run them both simultaneously to compare. However, the ability to move L/R would be helpful to hear things such as the tonal quality of the wire in the system.
The results using pairs should be as clear as when using individual cables. If you don't have a L/R balance control so that you can switch between them then I would not advise mismatching cables, as the result you would get would be less than ideal and at worst misleading toward each cable's sound.
