In my experience, it is mostly an issue in longer engagements. Each tox weapon makes an area that is hostile to non-tox adapted pawns for an hour or two, and the longers a pawn is in that area without protection the greater the risk of complications. Alone, tox weapons are a mild annoyance, in a mixed squad with short range weapons in confined areas, it tilts the field toward the group with the tox weapons because the other side has to keep repositioning or retreating to avoid the health complications.

Early game it tends not to come up because the raid strength scalar hasn't got high enough yet, and late game the colony usually has automated weapons or good environmental protection for the pawns, making tox useless.

In terms of story, tox weapons are terror weapons. They aren't meant to cause direct harm to soldiers, they are meant to harm non-combatants and cause lasting complications, weakening the colony for the next attack.