A character casting guidance to aid another character's ability check is basically like using the Help action.
The discussion about issues with Guidance
is entirely out-of-combat (in combat, action economy implies a cost to cast the cantrip, whereas out-of-combat it is completely free of cost), and out-of-combat the rules for "Working Together" still very much leave the DM full control over whether someone can help another.
But then again, the problem with Guidance
is that some DMs have seen players cast this cantrip every single time
someone is making a check, resulting in a cantrip which is far more useful than any other. If players would declare "work together!" every single time something is going on in the game, and the DM was forced to allow it, you would have the same problem.
And I think that's a fair interpretation as well. The easy counterpoint to "it works on passive checks" is that guidance says "one ability check you choose". If you argue that a character does not choose to do passive checks, its simply a consequence of other things going on, than even if the bonus is applicable, you could never choose to apply it.
I could see how that could also be used to prevent Guidance to work on almost every single reactive ability check. But I am not convinced because it says "of its choice" not "you choose", which means it is not referring to the fact that you have chosen to make the check, but rather than the target doesn't have to use Guidance of the first check it has to do but can choose to keep it for later.
I've actually never had a debate about guidance at my table. The one player whose character can cast it never pushes it and is quick to accept my ruling if there is doubt. (which is how it should be
At the root of the matter, is the fact that Guidance and Working Together were added to the rules under the designers' assumptions that they would be used occasionally, relying on the good faith of the players. It is only when a player realizes that by the RAW they can try to abuse these options, that they become a real problem. Some DMs are simply try to anticipate the problem.
I mean, unless you're in initiative outside of combat, things all happen simultaneously right? So you see an ally do a thing, you can act at the same time?
I mean otherwise, all that happens is this. Every turn the Cleric isn't doing anything else out of combat, he or she refreshes Guidance on their party members.
Right, if you want to cast the spell once every minute, I will then call you to make a perception check against traps every 5ft you move, everywhere and all the time. Do you see what is the annoyance here?