The default titlebar button order is "close:maximize". If a user decides to change it e.g. to ":maximize,close" via "org.pantheon.desktop.gala.appearance button-layout", this should influence the whole user environment -- move the close button to the right side also for the window overview, the workspace overview, some modal dialogs (see Maya, Noise), maybe even tab bars (see Terminal, Midori).
I acknowledge this is more of a design proposal and may be rather hard to implement. Nevertheless, I believe that design-wise, this could be elegant and user-friendly.
If it is not possible for all applications to follow Gala settings, another solution that comes to my mind is creating a new configuration switch in dconf for this case, something like "org.pantheon.desktop.dialogs close-button-position" with values "left" or "right"; though I am not a programmer. So far, I have not found a way how to configure this. If there is one, my appologies.
Yes, if possible Gala and Granite should probably try to find out which side of the window the close button is on and adjust accordingly.