Ian, going for a cube-cut on the flakes (even plugs) is more for flavor than burn quality or performance for me. Although the two might be slightly intertwined, come to think of it, which is why there is a flavor change...
...in any case, on my end, the draw is nearly identical and I don't notice a difference in condensation or heat between rubbing out or cube cutting, cubing just exposes more sides of each tobacco cube a bit more. Consistency in taste, if that's what one is after, can be had with some cube cutting, but often the dynamics and certain subtle flavors can't stand up and say "hello" quite as easily (and in those cases (or act like small flavor surprises), so I'll rub out a flake to a "chunky ribbon").
Cubes have never given me obstruction problems. The times I do have any kind of obstruction problems, I lightly cover the top of the chamber with my finger/thumb, puff strongly out through the stem, and back in again, and it dislodges any errant bits (which if left in there, can cause some awful moisture problems due to disruption of the airway during a smoke). A pipe cleaner to sweep/push out any offending bits works okay, too.
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