Thanks. In that case,
padding: 2px 1px 0px 0px;
should (vertically) match
padding: 1px 1px;
and it doesn't. Not even close. The second one works correctly. The first is utterly broken, with the spacing between folders being close to double the TEXT height, not double the PADDING. That's what I was trying to say before, but phrased very badly, sorry. The spacing between FILES with that first one is absolutely random, ranging from 2px to, again, double the text height.
Except, EUREKA, I've just found the pattern. 
With 2px 1px 0px 0px, IMAGE files are spaced (pretty much) correctly, but TEXT files have massive spacing - it's because of the vertical height of the icon! (This is in List View, which I should have made clear earlier, except it's the only sensible universal option despite not being the default (sigh), so I forgot there even WERE other display modes, sorry!)
I did also have a margin line in there at 0 0 0 0, which also made no difference so I pulled that too in the interest of simplicity / clarity / minimal random noise. I think there's quite a lot of copypasta in the theme files these days as a result of people struggling with GTK3 and just duplicating things. (I don't blame them at all).
I've got the same lack of knowledge re GTK's behavior, unfortunately. There doesn't seem to actually be any worthwhile documentation of it, and the corresponding pseudo-methods in the APIs also seem to just be doxygen generated and not really of any use to anyone unless they're already familiar with the actual implementation and just need their memory jogged.