Comment 38 for bug 170378

@~suv, you've made an horrible enough example :)
I see that the search doesn't work over layers (is it because they are managed as groups?).
Also, the two bottom right shapes are not selected with the others on the same layer because their transform attributes introduce rounding differences not shown in the "Fill and Stroke" dialog. My test case was much simpler, indeed. I admit that the PDFs you start from are much worse than mine ;)

Anyway, I wouldn't mind if the selection doesn't work here because there are so many heterogeneous objects (also if visually so much similar).
I'd move the problem into flatting the transform properties (is it possible? I don't know how to do), then selecting all inside a given tolerance (with the option we spoke about before) and finally really applying the same attributes to all, if this is the desired result. Personally I'd prefer not having all objects selected so I could spot unwanted transform attributes and get rid of them.
I agree that working with such files is legitimate, but I don't think they cover a big percentage of use cases to justify systematically loosing the matching criteria for everyone. Anyway, the tolerance settable to 0,0 should solve all this problems. Please, don't hesitate to correct me if I'm wrong.

In my opinion, the selection through layers should be added.