It's even worse than that: Gnome and KDE use very different standards, and some other Linux window managers vary from these too. For example, Gnome follows the Mac convention of placing the confirmation button of dialogs on the right, while KDE follows the Windows convention of placing the confirmation button on the left.
One can debate which is better supported by usability research, but there's no debating that deploying to multiple OSes, or even just multiple window managers on Linux, is a headache.
At the risk of appearing lazy, cross-platform developers have at least one thing going for them: while the Mac world is very picky about conforming to well-established standards, the Windows community has been dealing with all manner of non-standard UIs for so long that they're much more forgiving.
Sure, both OS vendors document their HIGs, but there seems to be a lot of disregard for the Win HIG in that developer community.
I've found that if you set the backgroundColor of your windows to the OS default and set the font face and size to the OS default, users are surprisingly forgiving about things like precise button sizing and placement.
In some cases I adjust layouts for different platforms, and Rev's Profile Manager is provided to help with that. But for many layouts I find Mac-compliant spacing is acceptable on Win, though doing it the other way around would bring shrieks of horror from the Mac audience.
If you deploy to Linux this approach also serves you well there, since Ubuntu is a leader among consumer installations and it ships with Gnome by default, which parallels Mac layouts well enough that things generally look more or less okay there.
Whether this is laziness or merely applying reasonable attention to ROI, Win sales of the products we make here relative to Mac are roughly proportionate to market share, and we've had zero comments from our customers on any platform-specific layout issues.