For this sort of stuff, booleans are a necessary evil to my mind. The thing to do is just make sure you have enough subdivision in the area that is to be sliced and diced so as to limit the triangulation. In your exhaust stack guard example, you should have shifted that entire top row of vertices that was cut by the boole object up a bit beforehand. The same goes for the bottom row, except it needed to be moved down. A little bit of triangulation is not the end of the world though on static objects like this. It's organic objects like faces that are subject to a lot of deformation during animation where problems really crop up. As long as you aren't getting any render artefacts then I wouldn't get too concerned with it.
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