Plugin dlls (iconengines, imageformats, platforms, qmltooling, QtQuick, QtQuick.2, sqldrivers, etc.) are copied to the wrong directory when running the following command to generate a Visual Studio 2013 project file:

qmake -tp vc <your project>.pro "CONFIG+=windeployqt"

The dlls are directly copied (no subdirectories are created) into
<projectname>\obj_qml\MDIL

During compilation in VS the compiler breaks with an error complaining that it cannot find the dlls:
#####
Error: Compile filter argument specified non-existent file: C:\development\test\obj_qml\MSIL\iconengines\qsvgicon.dll
Invalid argument

Microsoft (R) MDIL XAP Compiler - Version 4.0.0.0
Copyright (c) Microsoft Corporation. All rights reserved.

Usage: MDILXAPCompile /In:<InputPath> /Out:<OutputPath> /Config:<ConfigPath> [/CompileFilter:<Assembly Path>;<Assembly Path>] [/Timeout:<Timeout>] [/Log:<LogPath>] [/AppX]

/In - Path to directory containing files to process
/Out - Path to directory to place processed files in
/Config - Path to configuration file
/CompileFilter - Optional restrictive list of assembly files in InputPath,
separated by semi-colons, to be compiled.
/Timeout - Optional timeout in milliseconds before killing the Crossgen process. Overrides config file timeout value. Use -1 for infinite timeout, 0 for application default (2 hours).
/Log - Optional path to log file
/AppX - Specifies that assemblies correspond to an AppX package

Relative paths are relative to this executable's directory.
########
The solution is to manually copy all plugin directories into the "<projectname>\obj_qml\MDIL" directory.