There is overlap between the two -- but they are separate things.
The term "System Tray" is used exclusively in reference to this specific Windows interface idiom:
The System Tray has evolvedm from a skinny gulch of pixels over by the clock in Windows 95, into a sort of ongoing system-wide non-application party house. The task bar is arguably the Windows GUI equivalent of Fifth Avenue -- a famous and pleasantly grand thoroughfare, steering and endless stream of important traffic through prominent real estate. Contrastingly, the system tray is like the Bushwick warehouse party block, where all persistent background-process-ish things can pop up and act out a little. No one knows where their neighbors are from, but playing around with it feels meaningful enough; in fact it's actually almost endearing... but for the fact that it's constantly loud, and none of all those among its conspicuously myriad and visually distinctive guests seem in charge.
I have nothing against the System Tray; it may not be up for a Pritzker (if you will). The incidence of places like the System Tray -- utilitarian affairs that serve a number of important miscellaneous purposes fairly well -- are as common in the physical built environment as they are on our screens. Here's an analogous gathering-ground from my personal desktop:
Comparatively, a Notification Area is a more general idea. Notification Areas can be found across the major OSes in varied forms...
... and they are also de rigeur on web apps, from Facebook and Twitter on down through the ranks (which I won't trifle my fellow superusers with screenshots of those). The Windows System Tray is more than a Notification Area... in fact contains a Notification Area; my first recollection of this paradigm is of Windows 2000, and the rounded-rectangle cartoon-y balloon that told me A Network Cable [Was] Unplugged, so resolute with clockwork conviction and so frothingly eager because dammit, this is important information, so what if the network cable wasn't unplugged a couple of those times.
Remember all that? The System Tray has been around awhile and it's still there (for the moment, while it's still dark before the Windows 8-rise). It is always "The System Tray" rather than "one system tray" or "another", right? Whereas when you think of a Notification Area, it's yet another in a ceaseless line of notification areas, with little n's and little a's and enough of a visual twist to distract you from both the competing notifications from other areas and actual notification it's supposed to be serving you.
I can't imagine merging these two tags, because one of them is a specific interface that's been around long enough to have visibly evolved, and the other is a vaguer term for a range of elements. The idea of a Notification Area is more abstract, less mature, and explosively diverse than the System Tray: a widget with a familiar crooked smile, who everyone knows from around the way.