I personally feel a basic burners create pollution, and need vented away from or built away from machines, is a good place to start. implementation can be done in stages,
To put this into both flavor and functional:
Burners emit pollution that gets into chunk (functional part) AND a smog fluid block that works like thaumcraft taint (semi fluid-like block that floats side-upwards and can accumulate), if you're within it, you suffocate (flavor part). Once that smog block reaches sky (y=256), it disappears and turns into more pollution to the functional part.
This smog block has to be vented by keeping a way for it to flow upwards, which is easy unless you're living deep underground.
Muffler hatches and anything that could possibly pollute the air would do this.
Palladium catalysts would reduce the amount of smog blocks created.
Said smog blocks can also be destroyed with a scrubber machine should you require a self sustained enclosed system (for space stations and deep underground bases).