Technique for multifacteted roof without 3049
Would it be possible to just use a black one, or old dark gray? It would add a little variation to the roof, which is not a bad thing - it would look more natural. Perhaps the other color could be added to some other places here and there as well, so the colors all pull together nicely. 

Other than that you could always add a chimney, but as you mentioned you will have several places where you will face this issue. I can't think of any other piece that could serve the purpose exactly like 3049. You might also consider angled plates, which are other commony used pieces for roof-building. But without seeing your project it is hard to tell if that would work.