The coloured dots representing passenger destinations are not aligned with the underlying maps. The attached screenshot shows this in more detail. It appears to be an enlargement with scale factor slightly over 2 (more horizontally than vertically) about a centre to the left of and a little below the map origin. The attached image includes some lines I drew while trying to work out the transformation.
The map size is 640x512. I've also tested on maps of dimensions 320x320, 512x512, 256x256 and 192x128. It appears that the passenger dots are rendered as if a 256x256 portion of the world were being displayed (whether or not the actual game size is smaller/larger, and square/non-square). I can't account for why the lines I drew didn't converge at the origin, although it could be I misdrew them.
I also checked Standard (latest release, I think, not the nightly), and the maps appear to render correctly there.
I have to say, I did not know that the destinations map in the city window was big enough to be usable: it is not on larger maps, and even on smaller maps, one needs to enlarge the city window quite a lot for this to work. It seems to work on square maps (I think that it probably assumes that the map is square.
I should note that it is possible to view the passenger destinations on the main minimap by selecting the "destinations" overlay then clicking on the town hall of the town whose destinations that you want to track. This gives a larger (and thus clearer) display of the destinations than is possible in the city window, and is also zoomable.