I think it's also safe to presume that in the ultra future tech advanced society of Star Trek, they can remove the bacteria that causes body odor in humans.

A lot of odor-causing bacteria are actually beneficial for us though. And what causes Vulcans to experience that "odor" might not be coming from bacteria to begin with.. for all we know it might be one of the thousand of compounds that leak into the air we exhale directly from our lungs.

Virtually every gas or volatile liquid is susceptible to cause odor. The only reason we interpret pure water as odorless/tasteless is because water is everywhere so our senses evolved in a way that it doesn't trigger a response. There are many other compounds we don't really perceive because we are used to them at the concentrations that exist in our breath.

If let's say an alien species is not used to having 78% Nitrogen in their atmosphere, and they happen to have receptors sensible enough, then being in a ship with breathable air similar to Earth might just make them puke in disgust after having a sniff of what we might consider "clean air".

I'd argue it'd make more sense for everyone to wear the equivalent of a high tech mask (supressants?) rather than having to re-engineer the biology of the species every time they encounter an alien that might have a different set of compounds they might find unpleasant.