Nah, if you isolate the actual handle, you can run pixel retrievals and mouse clicks on each window separately, although you'd want to split them into separate processes! My little Immortal Bot manager in this forum somewhere is currently running separate scripts for each specific D3 window! You're welcome to download it and look at the auxiliary script folder and see how it works!
EDIT: Just realized I hadn't updated it so anything you looked at would have been useless! Here's the function!
Code:
Func MemoryReadPixel($x, $y, $handle)
Local $hDC
Local $iColor
Local $sColor
$hDC = _WinAPI_GetWindowDC($handle)
$iColor = DllCall("gdi32.dll", "int", "GetPixel", "int", $hDC, "int", $x, "int", $y)
$sColor = Hex($iColor[0], 6)
_WinAPI_ReleaseDC($handle, $hDC)
Return Hex("0x" & StringRight($sColor, 2) & StringMid($sColor, 3, 2) & StringLeft($sColor, 2))
EndFunc ;==>MemoryReadPixel