And yet, it's exactly like you say. It has nothing to do with the base widgets. The problem is that to look native on OS X, you have to use widgets that only exist on OS X, like their merged titlebar+toolbar that changes and resizes the entire window content used on preferences dialogs, or the blue left navigation sidepanel, or the big question mark button, or the segmented control, or the color selection popup menu with the wide color boxes in each list item, or the combo box zoom setting in one segment of the status bar.
And then your labels have to be right-justified while the controls are left-justified against those. You have to add about three times as much spacing between widgets as on other platforms. You have to have a single menubar that's outside the main window, and always has a "program name" menu where your preferences option has to be, a view menu, a window menu, and a help menu.
You have to be sure to tie in to all the OS X only things like AppleScript, Core(Image, Audio, ...), dialog sheets that slide down on a window and then are only modal to just that one window, etc. Your message boxes can't have titles anymore, but everywhere else expects one.
Even if you tried to add the extra spacing and hack in those OS X only widgets to Windows and Linux, then the Windows/Linux versions would be super hideous and unnatural. By the time you customize all of that, the code's a bigger mess than just making two separate GUIs. Defeats the entire purpose of using a cross-platform toolkit.
Bottom line is that Apple just does way too much stuff differently to be able to craft a cross-platform app that looks great everywhere with no platform-specific customizations.
And now Metro, Gnome 3, Unity and KDE 4/5 are trying to go in entirely different directions as well. And iOS and Android are big targets now, too. Sadly, the dream of write-once, run-anywhere and look nice is dead.