The start of page 46 says

"In general, banes or boons are generated based on the action being attempted first, then any other cards that are in effect, and finally special circumstances."

It then goes on to explain who decides how boons/banes are spent, and when, etc...

I keep re-reading that sentence and wonder if it is saying that, when boons/banes are generated, they are first applied to any boon/bane results listed on the action card, then onto any other cards (talents etc) then finally to anything that is left, until you run out of boons/banes or run out of effects to fuel.

So if there is an effect on an action card that is fuelled by two boons and you generate two boons in your roll, you have to activate that option in preference to regaining one stress/fatigue (a universal effect that can be fuelled by 2 boons).

Is this obvious and that's how everyone else has been playing anyway, and I'm just playing catch-up, or am I reading too much into that sentence, and its relevance is far less important; you apply the boon results to the effects you wish to in any order you wish to.

If it isn't saying that though, what is it saying?

The word generated doesn't make a great deal of sense a boons are generated based on the dice pool; there aren't any other effects that actually cause boons/banes to be added to a pool result are there? effects just add dice to a pool...don't they?

I think it's just making the general observation that it makes sense to place b/b effects close to the action when possible, and that you should probably look to the Action first to see what to spend them on, and then move outwards to Talents and Location and then go to general effects like the Fatigue/Stress thing. I think it makes sense narratively to look to the focus of the action and then outwards, but I don't think it is suggesting you've some kind of obligation to spend them there of you don't want to.

I don't play it that way intentionally, but I imagine if I analysed what i was doing, it might be that the vast majority of effects went on Action cards whenever possible. And I'd certainly have no objection if a player decided to overlook an Action card crit effect to regain some Fatigue, eg.

I think you are right.

After a few more reads, I felt the "In general" statement was inferring just what you describe, action cards are likely to be triggered by boons and banes on average more than others and in a narrative sense it makes sense to work through the options in that order, but for an specific boon/bane occurrence, exactly what the boon/banes are spent on is completely the players/GMs choice as appropriate.