I don't know that I can give a reliable consistent explanation since things just pour out of my head when writing :D I suppose one difference is - is it a long-term penalty, or is it just affecting the very next check? IIRC there's some exhaustion/injury scenarios where you are affected for the entire rest of the quest, so it gets a bigger notification to draw attention to it. Same with the quests where you can get a specific physical bonus before starting that lasts the whole quest through.
I don't remember where Stance comes in but most likely it can be positive OR negative depending. Tools, in the above example, is either a mild bonus, a nothing, or a mild penalty, depending on what you had to hand at the time. Sometimes, before attempting something difficult, Zorana goes through a whole list of things that might affect how well she does at whatever she's about to do, and all those checks add up to swing the final check, but they were clearly just about "can she do this one thing, how well prepared is she" so after the check where those bonuses are applied, they're not relevant anymore.
(IIRC in these cases I usually just wrote "bonus/penalty to the next check" in the script and Spiky came up with something to show it in the display)