As I see it, the Deep Dark would mess with the 'oreless' environment. The sound muffler would be nice, as would the ability to compress cobble, but the engines would completely remove any reason for the Buildcraft engine quest progression.
I never liked the deep dark so that's not an issue. As for the engines I fail to see how it removes anything. I still needed BC engines for pipes, and there for I made them and completed the quests. It seems that people think that players add mods to bypass/make something easier when that;s not the case. I still have completed and am using the bc engines because I am gating myself to better things. If I were to ever use the deep dark I would wait until I have an Botania Ore gen setup going strong before I went. Not to mention getting to the Deep Dark takes a LONG time even with 20+ cobble gens.lol You would have all the magical crops done by that time then who cares.lol